test 3

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Compare the three stages of sewage treatment process: TERTIARY

removal of inorganic materials achieved through chemical means and not with microbes

Transduction

type of HGT (horizontal gene transfer) that involves the transfer of genetic info from one bacteria to another via a virus (phage)

Lytic cycle

phage replication cycle resulting in the release of new phages by lysis (and death) of the host cell

Lysogenic cycle

phage replication cycle where the viral genome becomes incorporated into the bacterial host chromosome as a prophage and doesn't kill the host

Genes carried on plasmids. How plasmids are transferred between cells? what i

plasmids carry genes that cause diseases or convey antibiotic resistance genetic info is directly transferred btwn cells via a bridge-like structure called a *pilus* during conjugation

T/F To best isolate mutant bacteria that are threonine auxotrophs from a larger population, threonine-rich media should be inoculated and any colonies that form are presumptive auxotrophic mutants

False

T/F Transduction in this case is specialized rather than generalized.

False

T/F Transposable elements have been found only in prokaryotes and do not appear to play a major role in eukaryotes.

False

T/F Transposons are frequently used as cloning vectors.

False

T/F When a eukaryotic gene is expressed in a bacterium, the eukaryotic regulatory sequences should be maintained in order to achieve maximum expression of the gene.

False

The thermostable enzyme most commonly used in PCR is reverse transcriptase.

False

Transposons are frequently used as cloning vectors.

False

When a eukaryotic gene is expressed in a bacterium, the eukaryotic regulatory sequences should be maintained in order to achieve maximum expression of the gene.

False

Regardless of the exact approach taken to recombinant DNA technology, one of the keys to successful cloning is choosing the right vector.

True

Some plasmid vectors have incorporated the regulatory sequences of the lactose operon so that the expression of the recombinant gene can be induced at the appropriate time.

True

T/F . Approximately half of known animal carcinogens can be detected by the Ames test.

True

T/F A microbial ecologist who is interested in studying how gene expression is influenced by different species of bacteria in a biofilm would most likely find a metagenomic library more useful than a genomic library.

True

T/F Cosmids are plasmids that can be packaged into capsids of the bacteriophage lambda; therefore, they can be transmitted like phages, but they can exist and replicate in a cell like plasmids.

True

T/F Genes for antibiotic resistance can be found in antibiotic-producing bacteria as well as in non-antibiotic-producing bacteria.

True

T/F If 5-bromouracil was added to a culture of actively dividing bacterial cells, resulting mutations could eventually become a stable part of the cellular genome.

True

T/F In an HFR F+ mating, the conjugation bridge usually breaks before chromosomal transfer is complete. Therefore, the recipient remains F-.

True

T/F In the mechanics of conjugation, exclusive of gene transfer, Hfr and F+ strains behave the same.

True

T/F Photoreactivation repairs thymine dimers by splitting them back into separate thymines.

True

T/F Regardless of the exact approach taken to recombinant DNA technology, one of the keys to successful cloning is choosing the right vector.

True

T/F Some plasmid vectors have incorporated the regulatory sequences of the lactose operon so that the expression of the recombinant gene can be induced at the appropriate time.

True

T/F The Southern blotting technique for transferring DNA from an agarose gel to a piece of nitrocellulose membrane is named for E. M. Southern, the person who developed the procedure.

True

T/F When assessing the role of conjugative bacteria in the spread of antibiotic resistance genes, it is fair to say that Hfr cells contribute most while F- cells contribute least

True

The Southern blotting technique for transferring DNA from an agarose gel to a piece of nitrocellulose membrane is named for E. M. Southern, the person who developed the procedure.

True

Genetic material for viruses, DNA or RNA, single stranded or double stranded?

can be DNA or RNA (but not both) can be single or double stranded

Interon vs Exon

coding regions (exons) are interrupted by noncoding regions (introns).

If all of the PCR products of a DNA sequence are 4000 bp, then the DNA sequence that was amplified must have been 8000 bp.

false

Promoters for genes that code for proteins can be isolated from a cDNA library.

false

The thermostable enzyme most commonly used in PCR is reverse transcriptase.

false

Transposons are frequently used as cloning vectors.

false

When a eukaryotic gene is expressed in a bacterium, the eukaryotic regulatory sequences should be maintained in order to achieve maximum expression of the gene.

false

Four categories of antimicrobial drugs based on their mechanisms of action.

Inhibitors of cell wall synthesis Protein synthesis inhibitors Nucleic acid synthesis inhibitors Inhibitors of cell membrane function

A DNA molecule used to carry a foreign gene into a host organism is called a

vector

If chromosomal DNA from a host is the only type of DNA carried by a transducing particle, what can be concluded regarding transduction in this case?

Transduction in this case is generalized rather than specialized. -General transduction for pure DNA

Horizontal gene transfer.

Transfer of genes from one mature independent organism to another

Conjugation

Transfer of genetic information via direct cell-cell contact is called

Lysogen definition

a bacterium that contains a virus

Missense

a point mutation in which a *single nucleotide change results in a codon that codes for a different amino acid.* It is a type of nonsynonymous substitution. Often non-lethal and are the *driving force behind evolution*

transition mutation

a point mutation that changes a purine nucleotide to another purine (A ↔ G) or a pyrimidine nucleotide to another pyrimidine (C ↔ T). Usually due to base analogous

Neoplasia

abnormal new cell growth and reproduction due to loss of regulation

Silent Mutation

does not alter the amino acid sequence of the resulting protein

endonuclease

enzyme that cleaves internal phosphodiester bonds of a DNA molecule

Reverse Transcriptase

enzyme that turns single-stranded RNA into double-stranded DNA

___________ is a bacterial plasmid vector.

pUC19

The order of gene transfer in an Hfr F- mating is best represented by

part of the plasmid followed by the chromosome followed by the rest of the plasmid.

A microbial ecologist who is interested in studying how gene expression is influenced by different species of bacteria in a biofilm would most likely find a metagenomic library more useful than a genomic library.

true

Regardless of the exact approach taken to recombinant DNA technology, one of the keys to successful cloning is choosing the right vector.

true

Antibiotics effective against protein synthesis. Describe their modes of action

*Aminoglycoside* - binds to the 30S ribosomal subunit - directly inhibits protein synthesis, causes misreading errors - Ex: Streptomycin, gentamycin, erythromycin *Tetracyclines* - bind to the 30S ribosomal subunit - inhibits tRNA from binding to the ribosome *Macrolide antibiotics* - bind to the 50S - inhibit elongation of peptides *Chloramphenicol* - bind to the 50S - interferes w/ peptidyl transferase rxn

The PCR method was developed by

Mulis

Gene cloning

1 Isolate plasmid DNA from bacterial cell 2 Isolate DNA of interest 3 Insert gene of interest into plasmid DNA, which forms recombinant DNA 4 Insert recombinant DNA into bacterium such as Ecoli 5 Culture the bacteria, growing many identical copies

Lytic infection

AKA permissing infection/productive infection "standard" kind of viral infection virus infects the host and hijacks the cellular machinery to make more copies of itself and destroys the host by causing lysis influenza and polio

Antibiotics incorporated into the culture medium can A. select against organisms that have not incorporated the plasmid. B. select against organisms that have incorporated a plasmid not containing the desired gene. C. enhance production of recombinant proteins. D. select against organisms that have not incorporated the plasmid and select against organisms that have incorporated a plasmid not containing the desired gene

A. select against organisms that have not incorporated the plasmid

Transforming infections? List Viruses that cause cancer? Oncogenic Viruses?

Affects the host's genetic makeup, causing some kind of mutation in the host chromosome Often involves the integration of a viral genome at a point in the genome called an *oncogene*

Which type(s) of mutation might lead to a threonine auxotrophic revertant? A. All of the choices are correct. B. Base substitution C. Missense mutation D. Point mutation

Alltheabove

Allels

Alternate forms of genes resulting from mutations

List factors influencing effectiveness of antimicrobial drugs.

Amount that's administered Speed of uptake Rate of clearance from body Susceptibility of the pathogen Other hurdles such as: necrotic tissue/blood clots that prevent the drug from reaching its target

Restriction endonucleases in bacteria may have evolved in order to A. carry out natural genetic engineering. B. protect the bacteria from infection by viruses. C. use nucleic acids as a food (energy) source. D. all of the choices

B. protect the bacteria from infection by viruses

In silico analysis and annotation

Analysis carried out by a computer Annotation- used to determine where genes start and end, allows you to locate genes on the genome identifies ORF

Plasmid vectors often contain __________ genes that can be used to screen for recombinants

Antibiotic resistance

Describe ETest

Antibiotic sensitivity test manual in vitro diagnostic device used in labs to determine the MIC (minimum inhibitory concentration) and whether or not a specific strain of fungus or bacterium is susceptible to a particular antimicrobial agent

Autonomous replication?

Being able to replicate independently of the bacterial chromosome. Plasmids are capable of this.

The polymerase chain reaction (PCR) can be used to produce __________ of copies in a few hours.

Billions

Cloning a gene involves all of the following except A. isolating the fragment of DNA containing the desired gene. B. insertion of the gene into an appropriate vector. C. expression of the vector and the gene in a cell-free environment. D. introducing ligated DNA into E. coli cells.

C. expression of the vector and the gene in a cell-free environment.

Temin and Baltimore.

Discovered reverse transcriptase

Components of a virus. Name the two that every virus must have

EVERY virus must have a nucleic acid and a capsid SOME also have an envelope and spikes

Which is the most frequently chosen prokaryotic host for use in cloning techniques?

Escherichia coli

In an F+ F- conjugation, the donor is the __________ strain.

F+

After an F+ F- mating, the donor is __________ and the recipient is __________.

F+ , F-

Cosmids are so named because they can be used to express foreign genes in a variety of different hosts.

FALSE

A mutation from the most prevalent form of a gene to a mutant form is called a

Forward Mutation

Why are immunosuppressed individuals given antifungal agent?

Fungal infections are hard to diagnose in immunocompromised individuals- they can cause immortality Given as a preventative measure

Mutations that result in the death of an organism when expressed are called __________ mutations.

Leathal

Tumor

Growth or lump of tissue benign tumor remains in place

Credited with demonstrating unidirectional and nonreciprocal transfer of DNA between two mating E. coli cells

Hayes

When an F plasmid integrates into the host chromosome, the strain is referred to as

Hfr

Which situation(s) might warrant the removal of a histidine tag when purifying a recombinant protein?

Histidine residues inhibit protein folding, thereby decreasing the functionality of the protein.

The PCR method was developed by . Mullis.

Mullis.

Tools used in biotechnology and genetic engineering

In Silico analysis, DNA microarray analysis, gel electrophoresis, PCR, and RFLP analysis.

Role of reverse transcriptase in formation of provirus?

It converts the single stranded RNA to double stranded DNA. This enzyme is necessary for retroviruses to integrate into the host chromosome

Role of RNA in origin of life.

It has the ability to replicate and act as a catalyst for chem rxns it could have been the nucleic acid used in Earth's earliest life forms and RNA could have eventually given rise to DNA

Lethal mutations can be maintained in diploid organisms if they are

Recessive

An F' plasmid results when

an integrated F plasmid is incorrectly excised, bringing host genes with it.

pUC19

common cloning plasmid vector

What is Beta-Lactam ring? Which group of antibiotics contain beta lactam ring?

crucial feature of penicillins it binds to and inhibits enzymes responsible for the final step of bacterial cell wall synthesis (transpeptidation)

Exogenote

donor DNA that enters the bacterium by one of several mechanisms

A (n) __________ vector contains promoters that result in high-level transcription of the gene cloned within a multicloning site

expression

A (n) __________ vector contains promoters that result in high-level transcription of the gene cloned within a multicloning site.

expression

Antimicrobial drugs: Inhibitors of cell membrane function

impacts the assembly or proper functioning of the cell membrane

Conjugative transpons

may be involved in the spread of antibiotic resistance in bacteria.

Generalized Transduction

transfer of any bacterial gene to a recipient bacterium using a phage

Transduction

bacterial genes are transferred to another bacterium by a virus

Sub-microscopic, obligate intracellular parasite, and host specificity characterize viruses.

*Characteristics of Viruses:* sub-microscopic: can't see them with a microscope bc they're so small obligate intracellular parasites: can't grow or produce energy on their own, they require a host host specificity: specific viruses only attack a specific range of organism

Anti-fungal and anti-viral drugs

*Anti-viral:* Acyclovir (herpes) ribovirin (influenza) Amantadine (prevents virus from penetrating and uncoating) Tamiflu (shortens flu and prevents contagiousness) *Anti-fungal:* (targets ergosterol) azoles polyenes

Bio-Conversion, Biosensors, Biopolymers, Bio-Surfactants, and Biofuels

*Bio-conversion* AKA biotransformation Use of live organisms to facilitate a chemical reaction that converts a substance to a chemically modified form *Biosensors* Uses microorganisms, enzymes, or organelles and a physical transducer to detect the presence of a substance *Biopolymers* serve as gelling agents and modify the flow of liquids (ex: dextran or PHB) adding this to a fluid can slow it's movement through a system- industrial applications *Bio-surfactants* emulsify other substances such as oil useful in oil recovery, dispersing oil spills, bioremediation *Biofuels* microbial fermentation of crop residues consisting of cellulose and hemicellulose produces ethanol (a biofuel) which is widely used to power cars. Microbes also produce methane gas and hydrogen which can be used as biofuels.

Biocatalysts, bio-pesticides, GMOs

*Biocatalysts* microorganisms that facilitate changes to a substrate molecule but they aren't used up or changed as a result of the rxn Important to bioconversion! *Bio-pesticides* Naturally produced agents that kill pests *GMOs* living organisms whose genetic material has been artificially manipulated in a lab through genetic engineering

Bioprospecting and high-throughput screening (HTS)

*Bioprospecting*- the search for species that have medical and commercial use for humans (search in remote places like oil fields, rainforests, volcanoes, copper mines, hot springs) *HTS* allows researchers to rapidly and cheaply sequence and analyze a large amount of DNA

Viruses: enter, spread, and exit from the body?

*Entering:* -Mucous membranes: respiratory, genital, alimentary, or conjuctiva RESPIRATORY IS THE MOST COMMON ROUTE OF ENTRY -Skin: via wounds, scratches, insect bites *Spreading:* - Spread locally, over epithelial surfaces - Neurotropic viruses spread through nervous system (ex: rabies) - Lymphotrophic spreads through lymphatic system - Blood stream Viremia= when viruses are present in the blood stream - penetrating the skin (uncommon) - mother to fetus during pregnancy *Exiting:* Virus shedding= the many ways a virus can leave the body - sometimes a virus remains w/in the host and never sheds - through skin, feces, respiratory secretions, oropharyngeal secretions, etc point of exit isn't always the same as the point of entry

Human microbiome and explain the role metagenomics plays in its investigation.

*Human microbiome:* the aggregation of all the microorganisms that reside on or in the human body *Metagenomics:* Study of metagenomes (genetic material recovered from environmental samples) Used to study the composition of the human gut genome through analysis of fecal samples

Icosahedra and helical structures?

*Icosahedra shape* a polyhedron with 20 traingular faces, 30 edges, and 12 vertices made of capsomers *Helical shape* helical array of proteins wrapped around the nucleic acid

Cloning vectors used in creating Recombinant DNA.

*Plasmids* The most common type of cloning vector Plasmid- a self replicating piece of extrachromosomal DNA found in prokaryotes Popular bc they can be easily transferred from one organism to another via conjugation or transformation Typically carry inserted sequence in the mid-size range (20,000 base pairs or less). Ex: pBR322 and pUC19 *Bacteriophages* A virus that infects bacteria Carries smaller fragments ~9,000-25,000 base pairs *Cosmids* Is a hybrid btwn a plasmid and a phage. Carries larger fragments of ~30,000-47,000 base pairs *Artificial Chromosomes* Synthetic chromosomes that contain fragments of DNA integrated into a hose chromosome Categories: PI artificial chromosomes (PACs), bacterial artificial chromosomes (BACs), and yeast artificial chromosomes (YACs) Carries larger fragments YACs carry fragments up to 1million base pairs Used in the Human Genome Project

PCR

*Polymerase Chain Reaction* technique for quickly and easily making many copies of even a very small amount of DNA

Compare the three stages of sewage treatment process: PRIMARY

*Primary* Physically removing solid organic materials. the sludge is transferred to a large tank called an anaerobic digester where anaerobic methanogens degrade the organic molecules PRODUCES METHANE AS A BYPRODUCT methane gas burns very clean so plants use this gas as an energy source to generate electricity

Protoplast fusion? Electroporation? Transformation (plasmids picked up by laboratory-induced competent bacterial cells)

*Protoplast fusion* Scientists use enzymes or other means to remove cell walls of multiple cells, creating protoplasts Then put protoplasts together in solution and apply an electric shock (electroporation) which makes them fuse together to form a somatic hybrid (commonly used with fungi) *Transformation* -The direct uptake of genetic material from a bacterium's surroundings -Very rare in nature, commonly used in lab

Antibiotics effective against nucleic acid synthesis. Describe their modes of action

*Quinolones* - broad spectrum, synthetic drugs - inhibits DNA gyrase and DNA topoisomerase (which coils the DNA) *Rifampicin* - part of tuberculosis treatment - inhibits RNA polymerase *Ciprofloxacin*

RFLP?

*Restriction Fragment Length Polymorphism* Tool for genetic fingerprinting, genome mapping, localization of genes, paternity testing, and microbial classification Highly conserved and repetitive DNA sequences are present in nearly every genome, including genomes of humans, gram- and gram+ bacteria Uses fact that every organism has slightly different restriction sites so on the electrophoretic gel the patterns of restrictive fragments will vary Every person has a unique DNA fingerprint (useful for forensic evidence or paternity testing)

Give an example of how synergistic drug interaction between two drugs work

*Synergistic effect* 2 drugs work together to accomplish more than the additive effect of the two working separately *Trimethoprim and sulfonamides* (2 metabolic antagonists) often prescribed together to make treatment more efficient - sulfonamide is a structural analog and inhibits folic acid synthesis *Augmentin* combines amoxicillin and clavulanate potassium (beta-lactamase inhibitor) *Isoniazid and Rifampin* Isoniazid= antimetabolite Rifampin= nucleic acid inhibitor treats tuberculosis

Bacteria vs viruses

*Viruses* smaller than bacteria nonliving no cell walls or ribosomes not cellular requires host to replicate *Bacteria* living have cell walls have ribosomes cellular replicate on their own

Virus replication. What is the importance of un-coating step in viral infection

*attachment/adsorption* virus uses capsid or spikes to attach to receptors on host cell spikes act as ligands *penetration* virus injects genetic info into host sometimes nucleocapsid enters membrane also viral envelope is lost upon entry into the host cell *uncoating* If the viral capsid penetrates the cell, it must be shed inside the cell so as to expose the nucleic acid. After uncoating, the virus fuses with the endosome and the nucleic acid is released into the cell *synthesis/replication* viral genome is replicated and capsid proteins are produced *assembly* assembly of protein capsid around the nucleic acid core occurs within host *release* released into environment and considered virions

Microarray system. What is its purpose? Where the sample come from for this analysis (mRNA)

- Allows scientist to observe pattern of DNA expression for thousands of genes at a time. - Measure levels of specific RNA - Scan fluorescence, brightest= most RNA = most "active" genes - Monitor level of expression of every gene in a cell - DNA microarray- chips with a collection of tny DNA spots attached to a solid surface - Created by robotic machines that arrange hundreds or thousands of genes onto a single chip

Kirby-Bauer test and its purpose.

- Method for carrying out disk diffusion tests - for determining sensitivity of a bacterium to a particular antibiotic - bacterium grows on agar plate until it fills up - disk soaked in antibiotic is then placed on the plate - if bacterium is insensitive to the antibiotic, it will simply grow over the disk - if it IS sensitive, a "clear zone" will appear called a zone of inhibition (zone of no growth)

Properties of viruses given in slide 60.

- Obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals - estimated 10^31 virus particles on earth - Ubiquitous in nature and have had major impact on development of biological life - Ultramicroscopic in size - Acellular, structure is compact and economical - Don't independently fulfill characteristics of life - basic structure consists of protein shell (capsid) surrounding the nucleic acid core - molecules on virus surface have high specificity for attachment to host cell - multiply by taking control of host cell's genetic material and regulating synthesis and assembly of new viruses - lack enzymes for most metabolic processes -lack machinery for synthesizing proteins

Which of the following effects may be mediated by transposable elements

-A mutation may result from insertion into a gene. -Activation of nearby genes may occur. -Genetic deletions may form. (All the above)

Insertion sequences

-Normally relatively short (700 to 1,650 bp). -Capable of transposition. -Are discrete genetic elements bounded at both ends with inverted repeats.

Plaque assay technique steps

1 place few drops of host cells in plate with soft agar 2 allow host cells to grow to fill the entire plate 3 infect bacteria with virus 4 count # of viral plaques (clear areas) where the virus has killed a group of cells

Which of the following can be used as vectors for cloning DNA fragments?

A. plasmids B. cosmids C. bacteriophages D. All of the choices are correct.

Complete transfer in an Hfr F- mating takes approximately __________

100

A change in genotype, but not in phenotype, is most likely due to

A point mutation in the third position of a DNA triplet

Viral syndrome

A viral syndrome= a collection of signs and symptoms Ex of infections: oral, resp tract, skin rash, eye, hemorrhagic fevers, flu-like and systemic symptoms, gastroenteritis, hepatitis, CNS infection, STDs, congenital, perinatal, neonatal diseases

A transposable element composed of an antibiotic resistance gene, a recombinase gene, and inverted repeats is identified in a bacterial genome. This element can be any of the following except

A. an insertion sequence.

During the investigation of a convenience store robbery, witnesses report that the perpetrator exited through a main entry door without wearing gloves. The police are holding a prime suspect in custody while samples from the door are collected and analyzed for a DNA match. Since the door was handled by many people before the robbery, how will the forensics department distinguish the suspect's DNA from the DNA of others using PCR?

A- Sequence-specific primers to the suspect's DNA will be used for PCR amplification.

Which type of medium support growth of mutant bacteria that are threonine auxotrophs? A. Threonine auxotrophs only grow on media that is supplemented with threonine. B. Threonine auxotrophs only grow on media that lacks threonine. C. Since threonine is essential for growth, threonine auxotrophs do not grow on any type of media. D. Since threonine is essential for growth, threonine auxotrophs can grow on any type of media.

A- Threonine auxotrophs only grow on media that is supplemented with threonine.

A molecular biologist is interested in purify a recombinant protein by His-tagging, but the protein and vector both lack histidine residues. In this case, the molecular biologist could use which of the following technique(s) to acheive purification?

A. Add a 6xHis-tag to the C-terminus of the protein. B. Add a series of histidine residues to the N-terminus of the protein. C. Amplify the histidine-encoding sequence by PCR and add it to the gene of interest. D. All of the choices are correct.

Restriction endonucleases were discovered by A. Arber and Smith. B. Jackson, Symons, and Berg. C. Boyer and Cohen. D. Temin and Baltimore.

A. Arber and Smith

30. Which of the following types of cloning vector can carry the largest amount of foreign DNA? A. bacterial artificial chromosome B. bacteriophage C. cosmid D. plasmid

A. bacterial artificial chromosome

Which of the following bacterial hosts would should be used to avoid degradation of DNA that is introduced via a cloning vector? A. Escherichia coli that lack endonucleases B. RecA-expressing Escherchia coli C. Escherchia coli RecA mutants D. Saccharomyces cerevisiae wild type cells

A. Escherichia coli that lack endonucleases

Which of the following types of cloning vector can carry the largest amount of foreign DNA? A. bacterial artificial chromosome. B. bacteriophage. C. cosmid. D. plasmid.

A. bacterial artificial chromosome

Which situation(s) might warrant the removal of a histidine tag when purifying a recombinant protein?

A. Histidine residues inhibit protein folding, thereby decreasing the functionality of the protein.

You and a friend are student assistants in a research laboratory that investigates the anti-cancer properties of proteins isolated from marine organisms. Your friend mentions that she is using a BAC vector to insert shark DNA into Escherichia coli, but after repeated attempts, has found that the bacterial cells fail to synthesize the encoded protein. What is your advice? A. If the shark DNA is unmodified, it contains introns that are not recognized by bacteria, therefore protein synthesis will not occur.

A. If the shark DNA is unmodified, it contains introns that are not recognized by bacteria, therefore protein synthesis will not occur.

63. Which of the following is true of the integration of a viral genome into the host chromosome? A. Integration of the viral genome is a form of site-specific recombination. B. The enzymes that are used in integration are nonspecific for the virus and its host. C. Integration begins the process of host chromosome degradation. D. All of the choices are correct.

A. Integration of the viral genome is a form of site-specific recombination.

Site-specific recombination systems

A. do not depend on extensive nucleotide sequence homology. B. depend on enzymes that are often specific for sequences within the host. C. are features of some viruses. (All the above)

Which of the following techniques exemplifies phenotypic rescue in a host cell? A. Introducing a genomic library from a cell that produces a particular gene product into a mutant host cell auxotroph that cannot synthesize the product. B. Introducing a genomic library from a mutant cell auxotroph for a particular gene product into a host cell that can synthesize that product constitutively. C. Removing genes that encode a particular gene product from a cell that expresses that product constitutively before creating a genomic library. D. Replacing a mutant gene with a functional gene in a DNA library from an auxotrophic mutant cell prior to introducing the library into a related host cell.

A. Introducing a genomic library from a cell that produces a particular gene product into a mutant host cell auxotroph that cannot synthesize the product.

What would be the hypothetical outcome if the action of RecA were inhibited during the SOS response?

A. LexA would not autolyse, and therefore the transcription of DNA repair genes would not occur.

Which of the following terms is most closely related to genetic complementation? A. Phenotypic rescue B. Naked DNA C. Reverse transcription D. SOS response

A. Phenotypic rescue

Possible fates for an exogenote

A. integration into the host chromosome. B. independent replication and functioning. C. degradation to nucleotides. (All the above)

In order to express eukaryotic genes in a bacterium, the __________ must first be removed. A. introns B. exons C. enhancers D. 3' poly A sequence

A. introns

Which is a true statement regarding the size of PCR products? A. Since the number of DNA products ending exactly between both primers increases with each cycle, when PCR is completed, the majority of products are of similar size. B. Since the number of DNA products extends beyond each primer with each cycle, when PCR is completed, the majority of products are of various sizes. C. Since the length of primers increases with each cycle, when PCR is completed, the majority of products are of various sizes. D. None of the choices are correct.

A. Since the number of DNA products ending exactly between both primers increases with each cycle, when PCR is completed, the majority of products are of similar size.

Which is most analogous to the role of GFP in recombinant DNA technology?

A. Using dyes to stain and detect bacteria under light microscopy from the sputum of a patient diagnosed with tuberculosis. (GFP is green florescent protein, used to differentiate)

SOS repair

A. requires RecA protein. B. is inducible by DNA damage. C. is error prone, i.e., produces mutations (All the above)

Antibiotics incorporated into the culture medium can

A. select against organisms that have not incorporated the plasmid.

A (n) __________ vector is a plasmid that can be replicated in several different organisms because it has at least one origin of replication that will function in each host. A. shuttle B. chimeric C. expression D. phage

A. shuttle

Which of the following is not part of a yeast artificial chromosome (YAC)? A. The F factor. B. A selectable marker. C. An ARS. D. A CEN sequence.

A. the F factor

Which of the following is not part of a yeast artificial chromosome (YAC)? A. the F factor B. a selectable marker C. an ARS D. a CEN sequence

A. the F factor

Abortive infection

AKA non-productive infection virus is unable to successfully complete replication

Restriction endonucleases were discovered by

Arber and Smith

Three domains of microorganisms. Compare viruses with all other living things

Archaea, Bacteria, Eukarya Archaea and Bacteria include prokaryotes Eukaryotes: have diff ribosomes than prokart and lack gas vesicles mRNA contains introns and has to be further processed after transcription (prokr. mRNA doesn't) Viruses: acellular and nonliving rely on machinery and energy of their host cells to live an reproduce

An enzyme that cleaves internal phosphodiester bonds of a DNA molecule is a (n) A. exonuclease. B. endonuclease. C. ligase. D. methylase.

B. endonuclease

The three steps that take place in each cycle during PCR occur in which order? A. DNA annealing, denaturation, and synthesis. B. DNA denaturation, annealing, and synthesis. C. DNA synthesis, denaturation, and annealing. D. none of the above.

B. DNA denaturation, annealing, and synthesis

Recombinant DNA technology does not rely on which of the following enzymes? A. restriction endonucleases B. RNA methylase C. DNA ligase D. reverse transcriptase

B. RNA methylase

The PCR method was developed by A. Boyer. B. Mullis. C. Cohen. D. Sanger.

B. Mullis

Restriction endonucleases are produced by A. fungi. B. bacteria. C. protozoa. D. plants. E. All of the choices are correct.

B. bacteria.

21. Which of the following is not true of cloning vectors? A. They usually contain multicloning sites or polylinkers. B. They contain at least two replication origins. C. They can be replicated within an appropriate host. D. All of these are true of cloning vectors.

B. They contain at least two replication origins

Plasmid vectors often contain __________ genes that can be used to screen for recombinants. A. metabolic activation B. antibiotic resistance C. insertion sequence D. promoter/operator

B. antibiotic resistance

Restriction endonucleases are produced by A. fungi. B. bacteria. C. protozoa. D. plants. E. all of the choices

B. bacteria

When a eukaryotic gene is cloned into a bacterium, the advantage of a complementary DNA (cDNA) gene being used instead of fragments of genomic DNA is that A. the promoter and terminator are found in the cDNA gene but not in the genomic fragment. B. the introns have been removed from the cDNA gene but not from the genomic fragment. C. the cDNA is made with the nucleotides found in the prokaryote but not in the eukaryote. D. there is no advantage to using a cDNA gene rather than a genomic fragment.

B. the introns have been removed from the cDNA gene but not from the genomic fragment

Which of the following is not true of cloning vectors? A. They usually contain multicloning sites or polylinkers. B. They contain at least two replication origins. C. They can be replicated within an appropriate host. D. All of these are true of cloning vectors.

B. they contain at least two replication origins

Plasmid cloning vector DNA is usually introduced into bacterial hosts by A. ligation. B. transformation. C. transduction. D. plasmolysis.

B. transformation

A DNA molecule used to carry a foreign gene into a host organism is called a A. plasmid. B. vector. C. probe. D. blot.

B. vector

Mechanisms by which bacteria develop resistance to different anti-microbial drugs

Bacteria could develop ways to prevent antibiotic entrance into the cell, pump the drug out of the cell, modify the drug so it's ineffective, modify the structure that the drug acts on, or use an alternate pathway than the one the drug acts on mutation on chromosomal genome produce enzyme that inactivates drugs pump drugs out of cell before they're' effective exchanging plasmids

Microbes and the sulfur cycle

Bacteria engage in a number of redox rxns which cause the reduction of sulfur oxides to hydrogen sulfides

Bio-pesticides? Give an example.

Biopesticides = naturally produced agents that kill pests Ex: Bacillus thuringiensis (Bt) is a gram+ bacteria that produces a toxin (parasporal body). this kills a certain group of insects

. A microbiologist is working with two genera of bacteria, A and B, to determine if cells are competent. Strains are grown under optimal conditions, and DNA fragments that carry the gene for green fluorescent protein is added to each culture at 20-minute intervals. Samples from each treatment are plated to nutrient agar and incubated, after which the plates are examined under an ultraviolet lamp. The microbiologist observes that all plates of bacteria B contain colonies that are fluorescent, while for bacteria A only the plates from stationary phase demonstrate fluorescent colonies. What can be concluded from these results?

Both bacteria A and bacteria B cells are competent.

Which of the following is true about restriction endonucleases? A. They make a blunt cut on the two DNA strands so that there are no single-strand regions. B. They make staggered cuts on the DNA so that single-strand ends are formed that can be used to insert foreign DNA cut with the same enzyme. C. Some make a blunt cut on the two DNA strands so that there are no single-strand regions and some make staggered cuts on the DNA so that single-strand ends are formed that can be used to insert foreign DNA cut with the same enzyme. D. Depending on the incubation conditions, the same enzyme can either make a blunt cut on the two DNA strands so that there are no single-strand regions OR make staggered cuts on the DNA so that single-strand ends are formed that can be used to insert foreign DNA cut with the same enzyme.

A (n) __________ vector contains promoters that result in high-level transcription of the gene cloned within a multicloning site. A. shuttle B. chimeric C. expression D. phage

C. expression

Movement of charged molecules in an electrical field, which is used to separate nucleic acid fragments for recombinant DNA work, is called A. iontophoresis. B. nucleophoresis. C. electrophoresis. D. plasmaphoresis.

C. electrophoresis

C. expression of the vector and the gene in a cell-free environment

___________ is a bacterial plasmid vector. A. Lambda B. T4 DNA ligase C. pUC19 D. SV40

C. pUC19

A __________ is a DNA molecule used in hybridization reactions to detect the presence of a particular gene in separated DNA fragments. A. plasmid B. vector C. probe D. blot

C. probe

A PCR procedure that allows a determination of the amount of a particular DNA fragment that is present in a sample is called A. quantitative PCR. B. analytical PCR. C. real-time PCR. D. reverse PCR.

C. real-time PCR

Genetic manipulation

Changing the genome of an organism to produce desired traits

Chemotherapeutic agents? Which part of cells could be used as a target for antimicrobial agents

Chemotherapeutic agents include antibiotics and synthetic drugs that control the spread of microbes, either by killing them or preventing their proliferation. Used to fight diseases

Cloning?

Cloning is the process by which DNA sequence is isolated and replicated using a cloning vector.

What is the rationale behind the combination drug therapy for HIV infections?

Combination of drugs create obstacles to HIV replication This is why treatment for HIV involves at least 3 drugs from two diff classes

Medical significance of comparative genomics analysis? RFLP?

Comparative genomics studies the differences among the genomes of different organisms. Gives info about what makes a pathogen virulent and gives insights into what kinds of vaccines or therapies will be useful to fight against a virulent pathogen

CPE and give examples.

Cytopathic effects (CPE)= the effects of a viral infection that can be visualized with a microscope. *Examples:* - Viral plaque- visible area where virus has destroyed infected cells in a cell culture - Enlargement of either the cell, nucleus, or both - Membrane changes (greater elasticity) - Fusion of cells which produces a syncytium (multinucleate cell) - Leaky internal organs

Which of the following can be used as vectors for cloning DNA fragments? A. plasmids B. cosmids C. bacteriophages D. All of the choices are correct.

D All the above

Which of the following is not a strategy that bacteria use to resist the action of antibiotics? A. Modification of the antibiotic by the acetylation or phosphorylation. B. Cleavage of a key structural component of the antibiotic. C. Altering cell membrane structure to prevent antibiotic influx. D. All of the choices are correct.

D- All the above

Which of the following mutagens is most different than the others in terms of its effect on DNA? A. Acridine orange B. Intercalating agent C. Planar mutagen that inserts between stacked bases D. Base analogue

D. Base analogue

Which of the following bacterial hosts would should be used to avoid degradation of DNA that is introduced via a cloning vector?

Escherichia coli that lack endonucleases

The most frequently chosen prokaryotic host in cloning techniques is A. Saccharomyces cerevisiae. B. Bacillus subtilis. C. Staphylococcus aureus. D. Escherichia coli.

D. Escherichia coli

Which is the most frequently chosen prokaryotic host for use in cloning techniques? A. Saccharomyces cerevisiae B. Bacillus subtilis C. Staphylococcus aureus D. Escherichia coli

D. Escherichia coli

The enzyme reverse transcriptase was discovered by A. Arber and Smith. B. Jackson, Symons, and Berg. C. Boyer and Cohen. D. Temin and Baltimore.

D. Temin and Baltimore

Which of the following can be used as vectors for cloning DNA fragments? A. plasmids. B. cosmids. C. bacteriophages. D. all of the choices.

D. all of the choices

The polymerase chain reaction (PCR) can be used to produce __________ of copies in a few hours. A. hundreds B. thousands C. millions D. billions

D. billions

Which of the following was first produced commercially using recombinant DNA technology? A. Human growth hormone. B. Interleukins. C. Hepatitis B vaccine. D. Human insulin.

D. human insulin

Which of the following was first produced commercially using recombinant DNA technology? A. human growth hormone B. interleukins C. hepatitis B vaccine D. human insulin

D. human insulin

All of the following are appropriate strategies for overcoming drug resistance in bacteria except: A. decreasing the use of antibiotics in agriculture. B. patient compliance with dosage instructions when taking antibiotics. C. heightened infection control in health care facilities. D. prudent use of antibiotics when treating viral infections.

D. prudent use of antibiotics when treating viral infections.

Complementary DNA (cDNA) probes are produced using A. restriction endonucleases. B. RNA polymerase. C. DNA ligase. D. reverse transcriptase.

D. reverse transcriptase

Which of the following best describes the basis for separation of DNA fragments during agarose gel electrophoresis? A. The fragments with the highest percentage of G and C will migrate fastest. B. The fragments with the highest percentage of A and T will migrate fastest. C. The largest fragments will migrate fastest. D. The smallest fragments will migrate fastest.

D. the smallest fragments will migrate fastest

Recombinant DNA

DNA containing fragments from two or more different sources

cDNA

DNA copied from RNA by reverse transcriptase, lacks interons

The three steps that take place in each cycle during PCR occur

DNA denaturation, annealing, and synthesis

The three steps that take place in each cycle during PCR occur in which order?

DNA denaturation, annealing, and synthesis

Which of the following PCR procedures includes all of the others?

DNA is amplified for one cycle.

If a region of DNA contained numerous mismatches due to a modifying agent that caused methylation of guanine, which of the following mutagens is most likely the cause?

DNA modifier

Probe

DNA molecule used in hybridization reactions to detect the presence of a particular gene in separated DNA fragments

If DNA were a positively charged rather than negatively charged, what change to the gel electrophoresis procedure must be made?

DNA must be loaded at the positive pole rather than at the negative pole.

Repair of an apurinic or apyrimidinic site in DNA by AP endonuclease must be completed by the action of

DNA polymerase I

Complementary DNA (cDNA)

DNA produced from an RNA template using reverse transcriptase. often used to clone eukaryotic genes in prokaryotes. *Basic Process:* Begin with single stranded RNA and apply short poly-T primer Add reverse transcriptase and four nucleotides (ACGT) Add on enzyme called RNaseH to cut up the RNA and regenerate the RNA primers Add DNA polymerase and DNA ligase to synthesize a new strand

A public health microbiologist plans to screen a particular bacterial species that was isolated from several patients in an intensive care unit to detect if any of the cells are penicillin-resistant mutants. What is the first step in conducting this experiment? A. Determine whether or not wild type cells of the same bacterial species are susceptible to penicillin.

Determine if wild type (un-mutated)cells are penicillin resistant to begin with

Transformation

Direct uptake of genetic material ("naked") from the surroundings

Arber and Smith.

Discovered Restriction endonulases

History/origin of antibiotics? Why some microorganisms produce antibiotics

Discovered by Alexander Fleming in the 1920s (pencillin) Saved many thousands of lives during WWII Antibiotics are produced by bacteria and fungi as a natural defense mechanism against other bacteria

How one may prevent the emergence of drug resistant microbes?

Doctors can prescribe antibiotics in high enough concentration and in correct combination to kill all of the bacteria (giving 2 or more drugs at a time has synergistic effects) Doctors can prescribe fewer antibiotics Researchers can develop new drugs and treatments

In _____________, cells are mixed with recombinant DNA and exposed to a brief pulse of high-voltage electricity to cause the membrane to become permeable and allow the uptake of DNA from its environment.

Electroporation

Restriction enzymes

Endonucleases that cut double-stranded DNA at specific recognition sequences. Naturally produced by bacteria as a defense against viral infection, commonly used to create recombinant DNA

T/F The transformation frequency of very competent cells is about 10-6, or about 1 in 1,000,000 when an excess of DNA is used.

False

Cosmids are so named because they can be used to express foreign genes in a variety of different hosts.

False

Promoters for genes that code for proteins can be isolated from a cDNA library.

False

T/F A cell that is Hfr and a cell that is F+ can be the same cell

False

T/F Bacterial isolates from post surgical infections of several patients on the same hospital floor demonstrate an increase in resistance to similar antibiotics. The pattern of antibiotic resistance in these cases is most likely due to vertical gene transfer among bacteria that carry resistance genes to bacteria that lack those genes.

False

T/F In an F+ F- mating, all or part of the host chromosome usually is transferred to the recipient.

False

T/F One strategy to overcome antibiotic resistance is to use the same antibiotics in animal husbandry as those that are prescribed for humans, since the potential for resistant bacteria to evolve would be limited to only a small number of drug classes

False

T/F Stable integration of foreign DNA into a bacterial host genome is generally accomplished through induced plasmid transformation than by natural uptake of free DNA fragments.

False

Cloning a gene involves all of the following except

expression of the vector and the gene in a cell-free environment.

Industrial microbiology define fermentation? Compare Chemostat vs batch growth

Fermentation: the mass culture of microorganisms Chemostat: bioreactor in which the volume is kept constant by continuously adding fresh medium while removing the culture liquid Batch culture: technique for growing bacteria, bacteria grow until the limited supply of bacteria is used up

Genomics and list the three area of genomics

Genomics= study of the organization of genomes, the info they store, and the gene products they code for *Structural* study of physical nature of genomes *Functional* study of function of genomes - paralog= 2 or more genes found alike in the same genome that likely arose from gene duplication - ortholog= 2 or more genes very similar in different organisms, predicted to have the same function *Comparative* study of the differences among the genomes of diff organisms

A reciprocal exchange in which a pair of DNA with the same nucleotide sequence break and rejoin in a crossover is called __________ recombination.

Homologus (similar in position, structure)

Lytic vs lysogenic, why would a virus choose one over the other?

If it's lytic, it can quickly replicate and spread in the population BUT it could eventually kill all host cells and be without a host. Virus might opt for lysogenic cycle so that the host can survive and the virus can remain integrated in the host. It can then undergo induction when environmental conditions are right

If the shark DNA is unmodified, it contains introns that are not recognized by bacteria, therefore protein synthesis will not occur.

Which of these transposable elements do not carry genes for functions other than those needed for transposition?

Insertion Sequence

As pertaining to the spread of antibiotic resistance in bacteria, which of the following terms is not directly related to the others? A. Intercalate B. Cassette C. Integron D. Integrase

Intercalate (to insert)

A mutagen that inserts between the stacked bases of a DNA double helix, distorting the DNA to induce single-pair insertions or deletions is called a(n) __________ agent

Intercalating

In order to express eukaryotic genes in a bacterium, the __________ must first be removed.

Interons

Which of the following techniques exemplifies phenotypic rescue in a host cell?

Introducing a genomic library from a cell that produces a particular gene product into a mutant host cell auxotroph that cannot synthesize the product.

An insertion sequence is distinguishable from other mobile genetic elements because

It is smallest

Two-dimensional gel electrophoresis. What is it used for?

It uses electrophoretic gel to separate proteins based on 2 dimensions: charge and molecular mass pH gradient separates proteins by charge using isoelectric focusing, and gravity is used to separate based on mass *Process* Mix of proteins is loaded into an isoelectric focusing tube gel. (the gel consists of a pH gradient that separates proteins by charge) Proteins move around in the gel until their net charge is zero The isoelectric fell is laid on its side and the proteins move around until they're arranged by mass (small proteins travel farther down into the gel)

When separating DNA fragments by gel electrophoresis, what is the purpose of including molecular weight markers?

Markers are used as a control to determine the relative size of restriction fragments.

Name two groups of Archaea and describe their unique characteristics

Methanogenic archaea and extremely halophilic archaea (primarily chemoorganoheterotrophs that require a sodium chloride concentration of >1.5M)

Methanogens and what are their ecological and/or environmental impact

Methanogens produce methane as a metabolic product They live in anaerobic environments and are commonly found in the rumens of cows alongside grass Used by humans in sewage plants to digest sludge

What is the difference between methanogens and methanotrophs?

Methanotrophs- metabolize methane as their main source of carbon and energy Methanogens- produce methane as a metabolic byproduct

Microbes and the nitrogen cycle

Microbes convert one form of nitrogen to another Ex: denitrifying, nitrifying, nitrogen-fixing, and bacteria that assist in the decay of organic waste

Microbes and the phosphorus cycle

Microbes play NO role in this cycle

prototrophs

Microbes that can grow on minimal media/ synthesize own metabolites

Microbes and the carbon cycle

Microbial decomposition releases CO2 into the atmosphere Methanotrophs consume methane and methanogens produce methane

Monolayer in virus multiplication. List other culturing methods used to propagate viruses in laboratory

Monolayer: layer of homogenized cells growing side by side. If they're exposed to cancer cells, they will become "immortal" and can be used to propagate viruses Other method: growing viruses in entire organisms or in embryonated chicken eggs

Which procedure is most associated with unsuccessful transformation and degradation of DNA?

Natural Transfomation

Which of the following terms is most closely related to genetic complementation?

Phenotypic rescue

How do semisynthetic antibiotics differ from their parent molecules?

Often more effective than parent molec Ex: semisynthetic penicillin has a broader range than natural penicillin

Pasmid DNA having one EcoRI recognition sequence is treated with EcoRI restriction endonuclease. Following gel electrophoresis, how many bands should be visible on the gel?

One; plasmid is circular

Specialized transduction can be carried out

Only those temperate bacteriophages that integrate into the host chromosome.

Metabolic engineering? Explain DNA shuffling and whole genome shuffling.

Optimizing genetic processes in order to incr the production of a certain substance DNA shuffling: propagate beneficial mutations and incr size of a DNA library by randomly fragmenting a pool of related genes and reassembling those fragments Whole genome shuffling: use of protoplast fusion to introduce recombination throughout the entire genome

List the common reasons for increasing drug resistance and emergence of superbugs.

Over-prescription of antibiotics has selected against bacteria that lack resistance to drugs = leaving only drug-resistant bacteria in the population Result: greater # of bacteria is resistant to antibacterial drugs

If the att site of Escherichia coli was dissimilar to that of lambda phage due to a mutation, how would transduction be affected?

Phage DNA would be unable to integrate into host DNA

Temperate phage? What is their role in pathogenic microbe?

Phage that is capable of establishing lysogeny and integrating into the bacterial host Viruses can carry virulence genes that convey pathogenicity and help bacteria spread For it to produce more phage, induction must occur

What is composting? Do microbes have any role in this?

Process of decomposing organic matter and recycling it as fertilizer Soil is added to the organic matter in the compost to add microorganisms which help break down the organic matter

Recombinant DNA technology does not rely on which of the following enzymes?

RNA methylase

Recombinant DNA technology does not rely on which of the following enzymes? A. restriction endonucleases B. RNA methylase C. DNA ligase D. reverse transcriptase

RNA methylase

Transposons that insert at a new location while a copy remains at the original location are said to mediate _______________ transposition.

Replicative

Host __________ is the process by which some cells are capable of degrading an exogenote

Restriction

Recombinant plasmids

Restriction enzymes (cuts DNA of interest and bacterial plasmid at specific restriction sites, leaving fragments with sticky ends) cloning vectors DNA ligase (seals strands together by catalyzing phosphodiester bonds btwn single-strand breaks)

Which of the following is the most error-prone of the repair mechanisms A. Postreplication repair B. Recombination repair C. SOS repair D. Photoreactivation

SOS repair

How septic tank is compared to industrial sewage treatment process?

Septic tank= a holding tank for waste water, isn't a treatment system. Solid organic material falls to the bottom of the tank and settles, the tank has to be emptied after a few years MICROBES DON'T PLAY A ROLE IN THIS PROCESS

Sequence-specific primers to the suspect's DNA will be used for PCR amplification.

A (n) __________ vector is a plasmid that can be replicated in several different organisms because it has at least one origin of replication that will function in each host. A. shuttle

Shuttle

Which is a true statement regarding the size of PCR products?

Since the number of DNA products ending exactly between both primers increases with each cycle, when PCR is completed, the majority of products are of similar size.

The enzyme reverse transcriptase was discovered by

Temin and Baltimore.

When an F' plasmid acts as the donor in a mating, which of the following do(es) not happen?

Some chromosomal genes not on the plasmid are transferred.

55. Which of the following is true about restriction endonucleases? A. They make a blunt cut on the two DNA strands so that there are no single-strand regions. B. They make staggered cuts on the DNA so that single-strand ends are formed that can be used to insert foreign DNA cut with the same enzyme. C. Some make a blunt cut on the two DNA strands so that there are no single-strand regions and some make staggered cuts on the DNA so that single-strand ends are formed that can be used to insert foreign DNA cut with the same enzyme. D. Depending on the incubation conditions, the same enzyme can either make a blunt cut on the two DNA strands so that there are no single-strand regions OR make staggered cuts on the DNA so that single-strand ends are formed that can be used to insert foreign DNA cut with the same enzyme.

Some make a blunt cut on the two DNA strands so that there are no single-strand regions and some make staggered cuts on the DNA so that single-strand ends are formed that can be used to insert foreign DNA cut with the same enzyme

Which of the following is true about restriction endonucleases?

Proteomics?

Study of proteomes AKA entire collections of proteins produced by an organism

Functional genomics

Study of the function of genomes, how a genome works

Bioinformatics. What branch of science is involved in bioinformatics

Study of the genome using computers integrates computer science, biology, stats, math

Electroporation is commonly used to introduce recombinant DNA molecules into cells.

TRUE

Genetic engineering methods have been used to produce vaccines.

TRUE

If all of the restriction fragments in a DNA digest were of very low molecular weight, then all of the fragments on the electrophoretic gel will be closest to the positive pole and furthest from the negative pole.

TRUE

One of the major advantages to using plasmids as cloning vectors is that very high copy numbers can be achieved with many types of plasmid vectors.

TRUE

Some plasmid vectors have incorporated the regulatory sequences of the lactose operon so that the expression of the recombinant gene can be induced at the appropriate time.

TRUE

T/F If all of the restriction fragments in a DNA digest were of very low molecular weight, then all of the fragments on the electrophoretic gel will be closest to the positive pole and furthest from the negative pole.

TRUE

The Southern blotting technique for transferring DNA from an agarose gel to a piece of nitrocellulose membrane is named for E. M. Southern, the person who developed the procedure.

TRUE

he thermostable enzyme most commonly used in PCR

Tag Polymerase

Blotting

Technique that combines electrophoresis and hybridization to detect specific DNA fragments Southern = DNA Western = Protein Northern = RNA

Viral pathogenicity

The ability to: penetrate host cells grow within the cell fight against host cell's defense mechanisms damage the host

One of the major advantages to using plasmids as cloning vectors is that very high copy numbers can be achieved with many types of plasmid vectors.

True

An Hfr cell and an F- cell result from conjugation between a donor cell and a recipient cell. Which statement is false regarding this event?

The donor could have been either F- or F+.

Three basic principles of antimicrobial therapy

The drug must have selective toxicity for the target microbe Drug has to be able to reach the target at the right concentration Drug must be able to bind to and penetrate the cell, avoiding inactivation and extrusion

Which of the following conclusions can be made if two identical insertion sequences are identified in separate locations on a chromosome?

The insertion sequence was transferred via replicative transposition.

When a eukaryotic gene is cloned into a bacterium, the advantage of a complementary DNA (cDNA) gene being used instead of fragments of genomic DNA is that

The introns have been removed from the cDNA gene but not from the genomic fragment.

Which of the following is not true of specialized transduction? A. It is carried out by temperate phage. B. It is restricted to those genes on either side of an integrated prophage. C. The phage genome retains the full complement of phage genes. D. All of the choices are correct.

The phage genome retains the full complement of phage genes.

Generalized Transduction

The process by which foreign DNA is introduced into a cell by a virus or viral vector. *- The host chromosome is degraded into randomly sized fragments. - Any DNA fragment of the appropriate size is packaged. - Any bacterial gene may be transferred to the subsequent host. * (All the above)

Recombination

The process in which one or more nucleic acid molecules are rearranged or combined to produce a new nucleotide sequence

The major distinction between horizontal gene transfer and vertical gene transfer?

The recipient of genes in horizontal transfer is a mature cell, whereas the recipient of genes in vertical transfer is a progeny cell.

Which of the following best describes the basis for separation of DNA fragments during agarose gel electrophoresis?

The smallest fragments will migrate fastest.

Transforming infection

The virus affects the host's genetic makeup, causing some kind of mutation in the host chromosome

The utility of the strains of Salmonella typhimurium used in the Ames reversion assay because

They are highly permeable to test substances

Which of the following is not true of cloning vectors?

They contain at least two replication origins.

A molecular biologist treats a 600-kb length of linear DNA with HindIII restriction endonuclease. Following gel electrophoresis, the biologist observes that there is only one band on the gel corresponding with the migration distance of the 200-kb molecular weight marker. Assuming that no procedural errors were made, what can be concluded from these results?

Three HindIII recognition sequences were present in the original DNA.

What is the overall purpose of sewage treatment process? Why is treating sewage is necessary before releasing it in the environment?

To reduce the biological oxygen demand (BOD) = measure of amount of dissolved oxygen required by aerobic biological organisms in a body of water to break down the organic material in the water The more organic material in the water, the greater the biological oxygen demand= the more stress put on marine life Reducing BOD means sewage will support the growth of less bacteria Coliform bacteria is the most common to detect H2O contamination in the US

If chromosomal DNA from a host and phage DNA are carried by a transducing particle, what can be concluded regarding transduction in this case?

Transduction in this case is specialized rather than generalized.

Plasmid cloning vector DNA is usually introduced into bacterial hosts by

Transformation

When a recipient cell acquires a piece of naked DNA from the environment, it is called

Transformation

Cosmids are plasmids that can be packaged into capsids of the bacteriophage lambda; therefore, they can be transmitted like phages, but they can exist and replicate in a cell like plasmids.

True

Electroporation is commonly used to introduce recombinant DNA molecules into cells.

True

Genetic engineering methods have been used to produce vaccines.

True

Ti plasmid

Tumor-inducing plasmid (Ti) induces the formation of tumors in hundreds of plant species. Scientists found a way to take out the tumor-inducing genes and other non-essential regions. The plasmid can be used as a cloning vector

Whole genome shotgun sequencing?

Used for sequencing long DNA strands DNA is randomly broken up into numerous small segments and reassembled by computer programs by looking for regions of overlap (This was used to map the human genome!)

Which is most analogous to the role of GFP in recombinant DNA technology?

Using dyes to stain and detect bacteria under light microscopy from the sputum of a patient diagnosed with tuberculosis.

photoreactivation

Using light energy to repair thymine dimers

Sputum from a patient with a history of tuberculosis due to Mycobacterium tuberculosis bacteria is collected and sent to the microbiology lab for analysis. X-ray analysis and an acid-fast smear made from the sputum indicate that the patient has active tuberculosis. The physician has requested that the sputum be analyzed for pathogen load, but because colonies of Mycobacterium typically take between 3 to 8 weeks to appear on agar, results from traditional culture methods are often delayed. If you were the microbiologist in this case, what would you do?

Using the sputum, apply real-time PCR with primers to Mycobacterium tuberculosis DNA to estimate the pathogen load, then follow up with a traditional culture.

A DNA molecule used to carry a foreign gene into a host organism is called a

Vector

Which of the following methods of genetic recombination is common to both eukaryotic and bacterial cells?

Vertical Gene Transfer

One-Step growth cycle? What is the meaning of eclipse period?

a technique that involves exposing bacteria to viruses and then diluting the sample enough that no additional host cells will be infected by new viruses Eclipse period= there are no detectable infections viruses in the cell, although the virus is using the cell's internal machinery to produce the components needed to produce more viruses

Quantifying viruses in laboratory? Plaque assay? Hem-agglutination assay?

Virus quantification= counting the number of viruses in a specific volume to determine the concentration of viruses

Persistent infection

Virus reproduces slwoly and released by the cell slowly over a long period of time These infections don't abruptly kill the host as in a lytic infection

Explain why there are far fewer antiviral agents than there are antibacterial agents.

Viruses aren't metabolically active so they don't reproduce on their own. Drugs that fight against viruses must have their unique targets.

Virus multiplication vs growing bacteria.

Viruses require a host in order to replicate but bacterium can multiply on their own

The production of large quantities of a particular DNA sequence is known as gene

amplification

Which cloning vector should be used to express a 500-kb DNA fragment in Saccharomyces cerevisiae?

YAC

A microbiologist would like to use a noncompetent genus of streptococcal bacteria, Enterococcus faecalis, as a cloning host to express genes from Streptococcus pneumoniae, which is naturally competent. Is this possible?

Yes via artificial transformation (electroporation or chemical)

Yes; electroporation or chemical transformation can be used to make Enterococcus competent, and then genes from Streptococcus can be introduced via a cloning vector.

Selective toxicity. It is a term used to describe action of which molecules

ability of chemotherapeutic agents to exploit differences in the structures or metabolisms of microbes and of the host cells and inhibit or kill the pathogens w/o harming the host cells this is a key characteristic of useful microbial agent and describes the action of antibiotics

The production of large quantities of a particular DNA sequence is known as gene __________________.

amplification

Name three anaerobic environments where methanogens are found and are rich in organics.

animal rumens anaerobic sludge digesters anaerobic protozoa

Plasmid vectors often contain __________ genes that can be used to screen for recombinants.

antibiotic resistance

Which of the following types of cloning vector can carry the largest amount of foreign DNA?

bacterial artificial chromosome

A(n)__________ __________ is a piece of DNA with all of the features necessary for chromosomal replication and which can carry large (up to 1000 kb) pieces of foreign DNA into a host organism.

artificial chromosome

Restriction endonucleases are produced by

bacteria

The polymerase chain reaction (PCR) can be used to produce __________ of copies in a few hours.

billions

Lethal mutations can be recovered in haploid organisms if they are

conditional

Compare the three stages of sewage treatment process: DISINFECTION

disinfect water to remove all microbes ex: chlorination

How metabolic antagonists (antimetabolites) work?

disrupt steps in key metabolic pathways the drugs are typically structural analogs that resemble an actual molecule in the metabolic pathway but doesn't function like that molecule

Antimicrobial drugs: Protein synthesis inhibitors

disturb the process of protein synthesis, often targeting ribisomes Polymyxin B Aminoglycosdie Tetracyclines Macrolides Chloramphenicol

Movement of charged molecules in an electrical field, which is used to separate nucleic acid fragments for recombinant DNA work, is called

electrophoresis.

electroporation

An enzyme that cleaves internal phosphodiester bonds of a DNA molecule is a (n)

endonuclease.

PCR Primer

ensures amplification of the target DNA sequence only

Endogenote

genome of the recipient

Hemagglutination assay technique

hemagglutinin causes red blood cells to agglutinate (clump up) exposing a solution containing viruses to red blood cells and observe how much they clump up, researchers can quantify the red blood cells in the sample

Which of the following was first produced commercially using recombinant DNA

human insulin

Damages inflicted on host cells by viruses

inducing lysis (kills the cell) transforming the cell's genome altering nuclear or cytoplasmic structure of the hose altering gene expression int he host inhibiting RNA synthesis or synthesis of proteins using product of transcription (RNA molec) to construct new viruses rather than in normal gene expression for the host encouraging *apoptosis* (programmed cell death)

Viroid

inert version of the virus that exists outside of the host

Industrial and medical products produced via biotechnology

insulin alpha, beta, and gamma interferons alpha1-antritrypsin (treats emphysema) blood clotting factors (treats hemophilia) calcitonin (treats osteomalacia) focuses on producing primary and secondary metabolites for use as food, amino acids, antibiotics, and other purposes

Human peptide and proteins synthesized by genetic engineering

insulin (diabetes) alpha1- antitrypsin (emphysema) blood-clotting factors (hemophilia) calcitonin (osteomalacia) epidermal growth factor (wounds) erythropoietin (anemia) growth hormone interleukins (tumors and immune disorders) macrophage colony stimulating factor (cancer) relaxin (childbirth) serum albumin (plasma supplement) somatostatin (acromelagy) streptokinase and tissue plasminogen activator (anticoagulents) tumor necrosis factor (cancer)

In order to express eukaryotic genes in a bacterium, the __________ must first be removed.

introns

A genomic __________ is a sufficiently large collection of recombinant DNA molecules in which the inserted sequences together represent the entire genome of an organism.

library

Why protein synthesis (translation) excellent targets against some infectious diseases, but not others?

many antibiotics work by binding to the small (30S) or alrge (50S) subunits of the prokaryotic ribosomes, preventing them from assembling or carrying out their proper functions size and composition of prok/euk ribosomes differ, so antibiotics can effectively prevent protein synthesis in prok ribosomes while leaving the euk host's ribosomes unaffected

Real-time PCR

measure gene expression levels (quantity)

Plasmid DNA having one EcoRI recognition sequence is treated with EcoRI restriction endonuclease. Following gel electrophoresis, how many bands should be visible on the gel?

one

Antimicrobial drugs: Inhibitors of cell wall synthesis

prevent cells from proliferating by preventing synthesis of cell walls This is the most important target for antibiotics but is useless against bacteria that do not have cell walls Penicillins, cephalosporins, vancomycin, methicillin

Antimicrobial drugs: Nucleic acid synthesis inhibitors

prevent synthesis of DNA or RNA Quinolones Ciprofloxacin Rifampicin

Products made by microbes in industrial scale (industrial microbiology)

primary and secondary metabolites plant hormones food additives biopesticides genetically modified plants

Which of the following components of PCR ensures amplification of the target DNA sequence only, despite the presence of many other DNA sequences?

primers

A __________ is a DNA molecule used in hybridization reactions to detect the presence of a particular gene in separated DNA fragments.

probe

Restriction endonucleases in bacteria may have evolved in order to

protect the bacteria from infection by viruses.

Cloning vector

provides a mean for transferring genes of interest to a host organism during cloning.

Therapeutic index definition

ratio of the toxic dose to the therapeutic dose = toxic dose/therpeutic dose it's better for a drug to have a high therapeutic index bc it means overdosing is less likely to have negative consequences

A PCR procedure that allows a determination of the amount of a particular DNA fragment that is present in a sample is called

real time PCR

Which procedure is most useful in quantifying the active transcription of botulism toxin genes in a can of food that is contaminated?

real time PCR

Merozygote

recipient cell that is temporarily diploid as result of transfer process

Complementary DNA (cDNA) probes are produced using

reverse transcriptase.

Anaplasia

reversion to a more primitive or less differentiated state loss of cell differentiation

Antibiotics incorporated into the culture medium can

select against organisms that have not incorporated the plasmid.

Nonsense mutation

sense codon that corresponds to one of the twenty amino acids specified by the genetic code is *changed to a chain-terminating codon*

Gel electrophoresis

separates nucleic acids and proteins on the basis of their size and electrical charge, using a gel that is a polymer

A (n) __________ vector is a plasmid that can be replicated in several different organisms because it has at least one origin of replication that will function in each host.

shuttle

Prophage definition

specifically a virus that has infected a bacterial host latent form of a virus genome that remains with the host without destroying it

Metastasis

spread of cancerous cells throughout the body

Spectrum of activity

the # of diff pathogens a drug attacks can be narrow-spectrum or broad-spectrum

Which of the following is not part of a yeast artificial chromosome (YAC)?

the F factor

When a eukaryotic gene is cloned into a bacterium, the advantage of a complementary DNA (cDNA) gene being used instead of fragments of genomic DNA is that

the introns have been removed from the cDNA gene but not from the genomic fragment.

Therapeutic dose definition

the minimum drug level required for clinical treatment the minimum dose that is effective to achieve the desired results

Specialized Transduction

the transfer of a restricted set of only a few, specific bacterial genes to another bacterium via a phage

As a newly hired molecular biologist for a company that produces genetically modified seeds, your first project is to ensure that a GM cotton plant carrying a bacterial insecticide gene is expressed in tissues of seedlings as well as mature plants. To better understand regulation of the gene, you decide to use________ GFP fusion to detect activity of the promoter and also use_______ GFP fusion to determine the location of the protein in plants tissues at various stages of growth.

transcriptional; translational

Conjugation

transfer of genetic material between bacteria through direct contact

Name one mechanism by which resistance may spread through a bacterial population.

transferring R plasmids between bacteria

Plasmid cloning vector DNA is usually introduced into bacterial hosts by

transformation

Cosmids are plasmids that can be packaged into capsids of the bacteriophage lambda; therefore, they can be transmitted like phages, but they can exist and replicate in a cell like plasmids.

true

Reverse vaccinology works?

use of bioinformatics to screen the entire genome of a pathogen in order to identify genes that are good vaccine targets

Ames Test

used to measure the mutagenicity of chemicals.

Compare the three stages of sewage treatment process: SECONDARY

uses MICROBES to remove organic material from the liquid portion of sewage three major options: trickling filtration, activated sludge processing, and use of large lagoons REMOVES MOST OF THE BOD

Provirus definition

viral DNA that has been integrated into a host's chromosome

Latent infection

virus remains in the host cell in a dormant state until a trigger activates it and causes it to make more copies of itself HIV and Herpes

test 3

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