Bio 261 - Exam 2

How does a prion differ from a viroid? How does a prion differ from a virus?

A viroid is RNA with no protein b. A prion is a protein with no nucleic acid c. A virus contains both nucleic acid and protein

23. How is provirus different from a prophage?

prophage: phage viral DNA within the chromosome b. Provirus: animal viral DNA within the chromosome

What is unique about retroviruses? Name a retrovirus? Describe how retroviruses reproduce.

retroviruses: RNA viruses that replicate through a DNA intermediate (e.g., human immunodeficiency virus [HIV]) b. contain a reverse transcriptase (copies information from RNA to DNA), integrase, and protease c. enveloped

What are the basic components of a virus?

a nucleic acid genome i. Viruses can be classified on the basis of the hosts they infect. 1. bacterial viruses (bacteriophages; model systems) 2. archaeal viruses 3. animal viruses (extensively studied) 4. plant viruses (less well studied) b. a protein capsid that covers the genome. i. A capsid is almost always made up of repeating structural subunits that are arranged in one of two symmetrical structures, a helix or an icosahedron. In the simplest case, these "subunits" consist of a single polypeptide. In many cases, however, these structural subunits (also called protomers) are made up of several polypeptides. ii. Capsid and genome together are called the nucleocapsid c. In addition, many animal viruses contain a lipid envelope: i. lipoprotein membrane surrounding nucleocapsid ii. Enveloped viruses are formed by budding through cellular membranes, usually the plasma membrane but sometimes an internal membrane such as the ER, golgi, or nucleus. In these cases, the assembly of viral components (genome, capsid, matrix) occurs on the inside face of the membrane, the envelope glycoproteins cluster in that region of the membrane, and the virus buds out. This ability to bud allows the virus to exit the host cell without lysing, or killing the host. In contrast, non-enveloped viruses, and some enveloped viruses, kill the host cell in order to escape. d. The entire intact virus is called the virion. The structure and composition of these components can vary widely. i. exists outside host and facilitates transmission from one host cell to another

Distinguish between a capsid and a capsomere. What is a common symmetry for spherical viruses?

a. Capsid: the protein shell that surrounds the genome (nucleic acid: DNA or RNA) of a virus particle i. Capsids can be put together through self-assembly (spontaneous) or require host cell folding assistance. b. Capsomere: individual protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid making up the capsid c. Icosahedral symmetry is common for spherical viruses because it requires the fewest capsomeres.

What is the CRISPER system?

a. Clustered Regulatory Interspaced Short Palindromic Repeats b. Prokaryotic "immune system" that evades viral destruction and maintains genome stability i. Memory bank of incoming nucleic acid sequences for surveillance against foreign DNA (how they remember infections and are able to make proteins to prevent infections) c. Transcription of long RNA molecule cleaved in the middle of repeated sequences by nuclease activity of Cas proteins—generated CRISPR RNAs (crRNAs)—that base pair with invading nucleic acids, resulting in their destruction Transposons and insertion sequences—pieces of DNA that move around on chromosome and cause mutations SOS repair mechanism—how bacteria repair mutations (repair mechanism)

What is the divisome?​

a. Divisomes are made of interacting FtsZ proteins (which are crucial in binary fission) b. Cell division apparatus c. Forms about ¾ of the way into cell division d. Also contains Fts proteins crucial for peptidoglycan synthesis i. FtsI: penicillin-binding protein (activity inhibited by penicillin antibiotic) e. Orchestrates synthesis of new cytoplasmic membrane and cell wall material (division septum), the cell divides

What is EcoRI? What is it used for?

a. EcoRI is the restriction enzyme that cuts e. coli; gives us sticky ends

What is transpeptidation and why is it important to both the cell and clinical medicine?

a. Final step of peptidoglycan biosynthesis b. Forms the peptide cross-links between muramic acid residues in adjacent glycan chains c. In gram-negative bacteria, cross links form between diaminopimelic acid (DAP) on one peptide and D-alanine on adjacent peptide d. Removal of extra D-alanine from precursor is exergonic and drives transpeptidation forward e. In E. coli, FtsI is a transpeptidase f. Inhibited by the antibiotic penicillin i. Continued activity of autolysins weakens peptidoglycan and cell bursts

When an animal cell gets infected with a virus what are the possible consequences? How can a virus cause cancer?

virulent infection: lysis of host cell, most common b. Latent infection: Viral DNA exists in host genome and virions are not produced; host cell is unharmed unless/until virulence is triggered. c. Persistent infections: Release of virions from host cell by budding does not result in cell lysis. i. Infected cell remains alive and continues to produce virus d. transformation: Host cell conversion of normal cell into tumor cell i. Tumor cells are cells that have lost contact inhibition

What is a plaque-forming unit?

a measure of the number of particles capable of forming plaques per unit volume, such as virus particles.

What is an isoenzyme?

A different enzyme that catalyzes the same reaction but is subject to different regulatory controls

What is meant by a viral titer?

A titer: number of infectious units per volume of fluid

Where in the body do you fine adenoviruses?

Adenoids b. Both DNA strands are replicated c. dsDNA

What is the host cell for hepadnaviruses?​

Animal liver cell? b. Hepatitis B c. "serum" because it is spread in blood d. only partially double stranded RNA

Why are efflux pumps capable of conferring multidrug resistance?

Antibiotic resistance: efflux pumps and metabolic bypasses b. Efflux pumps are ubiquitous and transport various molecules, including antibiotics, out of the cell i. Lowers intracellular concentration, allowing cell to survive at higher external concentrations ii. act promiscuously and transport different classes outside the cell iii. contribute to multidrug resistance iiii. Acrobatic of E. coli is one of the best characterized and pumps out rifampicin, chloramphenicol, fluoroquinolones.

Describe at least two targets of antibiotics and discuss why the drugs are effective.

Antibiotics are antimicrobials naturally produced by microbes i. Kill or inhibit bacterial growth b. Target major molecular processes i. DNA replication, RNA synthesis, and translation 1. Quinolones target DNA gyrase and topoisomerase IV by interfering with DNA unwinding and replication 2. Rifampin and actinomycin prevent RNA synthesis by blocking RNA Polymerase active site of RNA elongation ii. Inhibition of protein synthesis iii. Ribosomes in Bacteria are 70S; eukaryotic are 80S 1. Puromycin binds to A site in 70S, inducing chain termination and inhibition protein synthesis 2. Aminoglycoside antibiotics (streptomycin) target 16S rRNA of 30S ribosomes, leading to error-filled proteins c. Target the cell membrane and wall i. Daptomycin specifically binds to phosphatidylglycerol resides of bacterial plasmid membrane, leading to pore formation, depolarization, and death ii. Polymyxins are cyclic peptides whose long tails target LPS layer, disrupting membrane and causing leakage and death iii. Targets peptidoglycan synthesis 1. B-lactams (penicillin, cephalosporin, derivatives) interfere with transpeptidation (formation of cross-links) 2. Vancomycin binds to pentapeptide precursor and prevents interbridge formation 3. Bacitracin binds to bactoprenol and prevents new peptidoglycan precursors from reaching site of synthesis

What is antigenic shift and drift? Which virus are they associated with and why do they occur?

Antigenic Shift: flu one and flu 2 join to form flu 3 (major change) i. Portions of the RNA genome from two genetically distinct strains of virus infecting the same cell are reassorted b. Antigenic Drift: flu one mutates to be flu ½ (slight change) i. Structure of neuraminidase and hemagglutinin proteins are subtly altered 1. Hemagglutinin causes clumping of red blood cells Neuraminidase breaks down sialic acid component of host cytoplasmic membrane c. Influenza (-RNA virus) i. Segmented genome (shift) 1. Segments of two different viruses infect the same cell (forms hybrid virus)

What are the four basic stages of biofilm formation?

Attachment i. Random collision ii. Facilitated by structures such as flagella and pili or by cell surface proteins iii. Signal for expression of biofilm-specific genes (encoding proteins that produce intercellular signaling molecules and extracellular polysaccharides) b. Colonization i. Signals guide bacteria in transitioning from planktonic growth to life in a semisolid matrix c. Development d. Dispersal

What are autolysins and why are they necessary?

Autolysins create small gaps for growing points by hydrolyzing bonds between N-acetylglucosamine and N-acetylmuramic acid b. New cell wall material is added across these gaps during insertion of new peptidoglycan c. Wall band: junction between new and old peptidoglycan on surface of gram-positive bacteria d. Important in the formation of new cell walls during binary fission

What is an auxotrophic mutant? How would you screen for it?

Auxotrophs have an additional nutritional requirement for growth b. Screen for it: i. Replica plating screens 1. Transfer colonies from master plate 2. Inability of colony to grow on a medium lacking a nutrient indicates mutation (selective medium) 3. Colony on master plate is picked, purified, characterized.

Why does attenuation control not occur in eukaryotes?

Eukaryotic transcription and translation do not occur simultaneously as they do in prokaryotic gene expression

What is a host? Bacteriophage?

Host: a living cell that the virus feeds off of. b. Bacteriophage: virus that infects bacteria

Name at least two common diseases caused by herpesviruses.

Latent virus b. Simplex I—cold sores; Simplex II—genital herpes c. Epstein Barr—mono d. HPV—genital warts, cervical cancer e. dsDNA

How does FtsZ find the cell midpoint of a rod shaped cell?

In rod-shaped cells, formation begins with attachment of FtsZ (related to tubulin; also found in virtually every Archaea) molecules around center of cell in a ring that becomes the cell division plane. b. The ring attracts other divisome proteins including FtsA (related to actin; recruits FtsZ and other divisome proteins and helps connect FtsZ ring to membrane) and ZipA (anchor that connects FtsZ ring to cytoplasmic membrane)

On what basis can prions be differentiated from all other infectious agents?

Infectious protein whose extracellular form contains no nucleic acid

Name some prion diseases and the organisms they are found in.

Kuru and Creudcezfield Jackob in humans b. Scrapies in sheep c. Mad cow in cows d. Wasting disease in moose and elk

What is feedback inhibition?

Mechanism for temporarily turning off the reactions in a biosynthetic pathway End product of the pathways binds to the first enzyme in the pathway, this inhibiting its activity Reversible reaction Inhibited enzyme is an allosteric enzyme

How do mutagens cause mutations? What are some examples of mutagens?

Mutagens—chemical, physical, or biological agents that increase mutation rates b. Chemical mutagens and radiation (major ones) i. nucleotide base analogs: resemble nucleotides but have faulty base-pairing due to a different side group 1. incorrect base pairing. Inhibit replication or cause mismatching. ii. chemical mutagens that induce chemical modifications 1. Athetium Bromide—stain used on DNA in gel then placed on UV light and bands fluoresce 2. Don't get it on skin because it causes mutation because it absorbs into skin and goes in the DNA to cause mutations that can lead to cancer (goes between base pairs) iii. nonionizing radiation (e.g., Ultraviolet [UV]) 1. Purines and pyrimidines strongly absorb UV. a. Pyrimidine dimer (two adjacent Cs or Ts on the same strand become covalently bonded) is primary effect of UV radiation. They base pair side to side rather than across 2. The longer and closer you encounter UV the higher chances of cancer iiii. ionizing radiation (e.g., X-rays, cosmic rays, and gamma rays) 1. more powerful than UV 2. Ionize water, forming free radicals such as hydroxyl radical (OH·) that damage macromolecules, leading to double- or single-stranded breaks and rearrangements or large deletions 3. Causes breaks in DNA that leads to mutations 4. Shorter the wavelength, the more penetrating the radiation (gamma)

What units are used to measure viruses?

Nanometers

What is the difference between the native and pathogenic forms of a prion protein?

Native prions live in the organism at all time and adapt to environmental conditions b. Pathogenic prions cause native prions to change their shape (and henceforth their function) i. leads to plaques and gray matter in brain c. nonpathogenic prions make non-lethal changes in fungi

Explain the term burst size.

Number of virions released after the one step growth curve that occurs when cells burst.

How does E. coli try to protect itself from phage attack, and how does T4 protect itself from these weapons?

Once phage DNA enters, E. coli has ways to prevent getting infected by making restriction enzymes that chop up DNA i. antiviral CRISPR ii. restriction endonucleases: enzymes that cleave foreign DNA at specific sites 1. Modification of host's own DNA at restriction enzyme recognition sites prevents cleavage of own DNA. 2. specific for dsDNA, so ssDNA and RNA viruses unaffected 3. Phage protection includes base substitution to resist restriction enzyme b. Modification of host's own DNA at restriction enzyme recognition sites prevents cleavage of own DNA.

What are phosphatases and what is their role in two-component regulatory systems?

Phosphatases—removes the phosphate from response regulator

Contrast mRNA production in the two classes of single stranded RNA viruses.

Positive strand is translated to viral proteins (RNA Polymerase, which copies the strand to make more viral DNA); positive copied into negative strand to provide a template for more positive strands b. Negative strand is copied to make a positive strand (template for more negative strands) by RNA Polymerase then translated into viral proteins c. RNA viruses are prone to mutation

What advantage do quorum-sensing systems confer on bacterial cells?

Prokaryotes can respond to the presence of other cells of the same species (assess population density) Ensures that a sufficient number of cells are present before initiating a response that, to be effective, requires a certain cell density Aids in biofilm formation, virulence factors Autoinducers produced by each bacterial species specifically diffuses freely across the cell envelope, it increases in internal concentration only if many cells are near by making the same autoinducer. Autoinducer binds to a specific activator protein or sensor kinase, triggering transcription of specific genes

How does MreB control the shape of a rod-shaped bacterium?

Prokaryotes contain a cell cytoskeleton that is dynamic and multifaceted b. MreB is a majer shape-determining factor in Bacteria and a few Archaea c. Forms simple cytoskeleton with patchlike filaments around inside of cell just below the cytoplasmic membrane d. Recruits other proteins for cell wall growth to group into a specific pattern e. Inactivation causes cells to become cocci i. Most cocci lack MreB f. Filaments move from one side to another, localizing synthesis of peptidoglycan and allowing new cell wall to form at several points

What is rBST and how is it made? What is it used for?

Recombinant bovine somatotropin: The gene that expresses bST is inserted into a bacterium using the recombinant DNA technique. This bacterium can then produce a hormone identical to bST, which is called rbST. a. commonly used in dairy industry; stimulates milk production in cows

Why does a virus need a host cell?

Replication and reproduction occurs only upon infection (entry into host cell)

What are the advantages of using super-resolution microscopy vs standard fluorescence microscopy?

Resolution is 10-50nm b. Observes dynamic behaviors in real time c. Can resolve multiple proteins, different nucleic acids, different loci within one nucleic acid molecule (when combined with fluorescent tagging)

Compare and contrast the various types of viral replication.

Retroviral Replication b. Positive and negative strand RNA replication c. DNA Replication

What type of virus is HIV? What does it cause?

Retrovirus b. RNA virus c. Infects T-helper lymphocytes d. Leads to AIDS, breakdown of immune system

What is unusual about genetic information flow in retroviruss?

Retroviruses use reverse transcriptase enzyme to turn a ssRNA into dsDNA then go into a provirus stage

. What is the shaped and name of the virus that causes rabies? What type of virus is it?

Rhabdovirus b. Bullet shaped, enveloped, helical nucleocapsid containing several enzymes c. dsRNA virus

Distinguish between screening and selection.

Selectable mutations—confer an advantage; mutant children can outgrow and replace parent under certain environmental conditions i. Ex. Antibiotic resistance b. Screening mutations—do NOT confer an advantage even though a phenotypic change may occur; requires laborious, time-consuming screening (examining large numbers and looking for differences) to find i. Ex. Color loss in a pigmented organism

What is the difference between an allosteric site and an active site?

The active site is where a substrate binds in order for the enzyme to do its purpose An allosteric site is where an inhibitor binds to change the conformation of the enzyme's active site so that substrates cannot bind and the enzyme cannot fulfill its purpose

What would happen to regulation from a promoter under negative control if the region where the regulatory protein binds was deleted? What if the promoter was under positive control?

Transcription would not happen Transcription would occur

Describe a complex virus and give an example.

The most complex of all viruses are the head-plus-tail bacteriophages that infect Escherichia coli , such as phage T4. A T4 virion consists of an icosahedral head plus a helical tail (see Figures 8.19 and 8.20). Some large viruses that infect eukaryotes are also structurally complex, although in ways quite distinct from the headplus-tail bacteriophages. The most complex viral penetration mechanisms exist with the tailed bacteriophages. Bacteriophage T4 consists of an icosahedral head, within which the viral linear double-stranded DNA is folded, and a long, complex tail, which ends in a series of tail fibers and tail pins that contact the cell surface. Phage T4 virions first attach to Escherichia coli cells using their tail fibers (Figure 8.11 ). The ends of the tail fibers interact specifically with polysaccharides in the cell's LPS layer and then the tail fibers retract, allowing the tail itself to contact the cell wall via the tail pins. The activity of T4 lysozyme then forms a small pore in the peptidoglycan layer and the tail sheath contracts. When this occurs, T4 DNA enters the cytoplasm of the E. coli cell through a tail tube in a fashion resembling that of injection by a syringe. By contrast, the T4 capsid remains outside the cell (Figure 8.11). DNA inside bacteriophage heads is under high pressure, and because the interior of a bacterial cell is also under pressure from osmotic forces, the phage DNA injection process takes several minutes to complete. The virus encodes its own DNA polymerase.

Why is the latent period so named?

The pathogen is present in a 'latent' stage, without clinical symptoms or signs of infection in the host.

What is the difference between generalized and specialized transduction?

a. Generalized—DNA any portion of the host genome is packaged inside the virion (lytic phage) i. initiated during the lytic cycle ii. not very efficient b. Specialized—DNA from a specific region of the host chromosome is integrated directly into the virus genome (latent phage) i. May be integrated during lysogeny, or homologous recombination may occur ii. Initiated during the lysogenic cycle iii. Very efficient iiii. Takes genes of host on either side of the viral DNA with it

What are viroids and what do they infect?

a. Infectious RNA molecules that lack a protein component b. Small, circular, ssRNA c. Smallest known pathogens d. Plant diseases; the plant must have a cut or other opening for them to enter e. Most symptoms are growth-related i. Moves throughout plant cell interfering with growth

What is the function of bactoprenol?

a. Insertion of new peptidoglycan i. Plays a major role in precursor insertion ii. Hydrophobic C55 alcohol iii. Bonds to N-acetylglucosamine/N-acetylmuramic acid/pentapeptide peptidoglycan precursor iiii. Transports precursors across membrane b. Outside of the cell, bactoprenol complex interacts with transglycosylases that insert peptidoglycan precursors into growing points and catalyze glycosidic bond formation

What is the advantage of using genetic engineering to make insulin?

a. Insulin is used to treat diabetes. Genetic engineered insulin is easier to create high quantities of and is less likely to cause an adverse reaction.

How is a lytic virus different from a latent virus? What other terms are used to describe latent viruses?

a. Lysogenic infection happens when viral DNA gets into host DNA and replicates i. Lysogenic, latent, and temperate all mean the same thing: viral nucleic acid is incorporated into the host chromosome 1. Means it is just sitting there, not making new viruses; repressor proteins keep the DNA within the host DNA so virions are not produces 2. Host cell is not harmed unless virulence is triggered ii. Phages like lambda are called prophage iii. Animal viruses like HIV are called proviruses b. Virulent (lytic) infections reproduce themselves and lyse the host i. T4 is a living bacteriophage which lyses its host E. coli after it has reproduced

Why do frameshift mutations generally have more serious consequences than missense mutations?

a. Missense mutation changes the sequence of amino acids in a polypeptide (base pair substitution) i. Codes for an entirely different amino acid b. Frameshift mutations i. Deletions or insertions that result in a shift in the reading frame ii. May be one single base pair, or three (entire amino acid) at a time (up to thousands of base pairs) iii. Changes the entire sequence of polypeptide downstream (changes codons which changes amino acids which changes the protein) iiii. Often result in complete loss of gene function c. Point mutation i. Happens because of one base d. Silent mutation i. Change in bases, but coded for the same amino acid (no phenotypic change) e. Nonsense i. Codes for a stop codon f. Wild Type is what you find in nature i. Reversions are when mutations lead to mutant going back to the wild type

Why is PUC19 a great cloning vector?

a. Molecular cloning—movement of a gene from original source to small and manipulatable genetic element (vector) i. Results in recombinant DNA ii. Gene can be manipulated iii. Cloned DNA replicated b. PUC19 i. Plasmid that is widely used ii. Restriction enzyme with cut site within MCS chosen iii. Vector and foreign DNA cut with the enzyme iiii. DNA ligase used v. Insertional inactivation of gene within lacZ distrupts gene and detecs cloned DNA vi. Transformants plated on media containing ampicillin and X-gal (turns blue) to detect Beta galactosidase activity vii. Cell containing vector and insert are white

Distinguish between a mutation and a mutant.

a. Mutation—A heritable change in DNA sequence that can lead to a change in phenotype (indicated by 3 lowercase and 2 uppercase) b. Mutant—a cell or virus derived from a wild type that carries a nucleotide (genotype) sequence change (phenotypic change represented by a +/-)

What is the difference between a naked virus and an enveloped virus?

a. Naked virus: nucleic acid with nothing else besides a protein coat b. Enveloped viruses (e.g., many animal viruses) have an outer layer consisting of a phospholipid bilayer (from host cell membrane) and viral proteins. i. Enveloped viruses bud out of the cell, taking the membrane with it ii. HIV is an enveloped virus; the host of HIV is the T Helper cell iii. When the t cell count is below 200 you are immunocomprimised and will get sick from anything

How does PCR work and when would you use it? What is Taq? Where did it come from and why is that beneficial?

a. PCR—polymerase chain reaction is DNA replication in vitro, multiplying segments of target DNA up to a billionfold during amplification (doubling) i. Thermocylcer—automated PCR machine ii. Requires DNA polymerase and artificial oligonucleotide primers made of DNA iii. Amplifies stretches of a few kbp target from within a template 1. Denature template DNA by heating and add two DNA oligonucleotide primers in excess 2. DNA poly extends primers using template DNA 3. Heat to separate strands and cool 4. Repated 20-30 times yielding 106 to 109 fold increase b. Taq is a thermostable DNA polymerase that is critical to PCR because it has resistance to high temperatures c. Applications i. Cloning or sequencing, phylogenetic studies, amplifying very small DNA quantities, medical diagnostics, forensic science ii. Reverse transcription PCR​ 1. Can make DNA from an mRNA template 2. Uses the enzyme reverse transcriptase to convert RNA into complementary DNA

Distinguish between a positive-strand RNA virus and a negative strand RNA virus.

a. Positive are the same as mRNA and can be directly translated b. Negative are complementary to mRNA and must be copied before translated

Explain why recombinant vaccines might be safer than some vaccines produced by tradition methods?

a. Recombinant vaccines can: i. Modify a pathogen with genetic engineering to delete virulence factors and retain those that elicit immune response ii. Engineer genes from a pathogenic virus to genome of a harmless carrier virus iii. Polyvalent vaccine: single vaccine that immunizes against two different diseases

What is a reporter gene? The product of which reporter gene yields a green color?

a. Reporter genes encode protein easy to detect and assay i. May be used to report presence/absence of a genetic element in a vector ii. Can be fused to other genes or other gene promoters to study gene expression iii. First widely used was lacZ from E. coli encoding β-galactosidase. b. Green fluorescent protein (GFP)

What are reporter genes and why are they useful?

a. Reporter genes encode proteins for an easy-to-detect or assay and are fused to genes of interest, enabling visualization of proteins and monitoring gene expression b. Ex. Green fluorescent protein

What are the important differences among a recombinant live attenuated vaccine, a vector vaccine and a subunit vaccine?

a. Subunit vaccines contain only a specific protein or proteins from a pathogenic organism (ex. Coat protein of a virus) i. Popular bc large amounts of immunogenic proteins can be administered at high dosage with less risk than attenuated or killed vaccines b. Vector Vaccines induce immunity to a pathogen by way of a harmless carrier virus

Why does phage T4 need a lysozyme-like protein in order to infect its host, and what part of T4 enter the host cytoplasm?

a. T4 Is a double stranded DNA virus and attaches to the LPS of the polysaccharide membrane b. Virions attach to cells via tail fibers that interact with polysaccharides on E. coli LPS layer. c. Tail fibers retract, and tail pins contact cell wall. d. T4 lysozyme forms small pore in peptidoglycan. e. Tail sheath contracts, and viral DNA passes into cytoplasm. f. Capside stays outside.

Explain how you could clone a gene for insulin production into E. coli.

a. The human insulin gene has been cloned into a plasmid vector and expressed in E. coli. Large amounts of insulin can then be produced and used to treat diabetes. b. Scientists build the human insulin gene in the laboratory. Then they remove a loop of bacterial DNA known as a plasmid and insert the human insulin gene into the plasmid. Researchers return the plasmid to the bacteria (e. coli) and put the "recombinant" bacteria in large fermentation tanks. There, the recombinant bacteria use the gene to begin producing human insulin. cientists harvest the insulin from the bacteria and purify the substance for use as a medicine for people.

What is packaged into capsids during maturation?

a. The viral genome is inserted into the capsid to form a nucleocapsid, which then undergoes some type of maturation that can include proteolytic cleavage of capsid proteins. In the case of non-enveloped viruses, these newly formed virions accumulate in the cell and are released by cell lysis.

How does a transducing particle differ from an infectious bacteriophage?

a. Transduction—transfer of host cell DNA from one cell to another by way of a bacteriophage b. Phage is ineffective (cant infect) because it has host DNA not viral—transducing phage

Explain how transformation works. What is meant by competence in genetic transformation experiments.

a. Transformation—genetic transfer process by which free DNA is incorporated into a recipient cell and brings about genetic change (uptake of free DNA) i. Natural transformation starts with reversible DNA binding that becomes irreversible 1. Competent cells bind up to 1000x more DNA than noncompetent cells 2. Strep are naturally competent 3. E. coli must be made competent b. Competency—a cell that can take up DNA and be transformed; capability to do this is genetically determined c. In naturally transformable bacteria, competence is regulated and competence-specific proteins uptake and process DNA d. In other strains, specific procedures are necessary to make cells competent (growing them in cold calcium) e. Free DNA comes from cells that have lysed; a plasmid (vector because it carries genes) f. Griffith Study: i. Smooth cells had a capsule (strep pneumonia) ii. Live rough cells mixed with dead smooth cells bc smooth cells that had capsule gene in a plasmid transferred the plasmid to the rough (rough are competent iii. Once the rough took up the capsule, they became infectious by avoiding phagocytosis and caused pneumonia in mouse that killed it

What is a transgenic plant?

a. Transgenic—genetically engineered organism that contains a gene (transgene) from another organism b. Ti plasmid contains genes that mobilize DNA for transfer to plant; responsible for virulence i. T-DNA: plasmid segment transferred to plant; sequences at ends essential for transfer

How does a virus differ from a cell?

a. Viruses are not cells because they have both DNA and RNA, they have to have a host, and don't reproduce independently i. They choose their host by recognizing certain receptors on it

Compare and contrast conjugation and Hfr conjugation.

a. When F plasmids become integrated into a host chromosome they become Hfr (high frequency of recombination) i. Pili are used for conjugation; DNA transfer begins in the middle of F factor in host chromosome and normally breaks before completion, so the recipient is still an F- cell; the F genes that are in the recipient integrate into the host chromosome (host chromosome DNA is also transferred) b. Nonintegrated F plasmids used in regular conjugation are called F+ i. Pilli are used for conjugation; single stranded copy of the F+ plasmid is transferred, each cell synthesized a complementary strand and contains a full F plasmid

Describe two ways that prokaryotic cells can avoid viral infection and how viruses may overcome these defenses.

a. alterations in viral receptor sites: modification of receptor or protection with a shield such as a capsule b. Viruses can mutate or degrade capsule. c. Some temperate bacteriophages hijack host's toxin-antitoxin system. d. Both the virus and the host cell evolve e. HERV—when pieces of retrovirus DNA are left inside the host DNA; linked to autoimmune disorders

How is T4 and Lambda similar and different?

a. both are phages and have double-strand DNA b. T4=lytic virus (kills host) and injects DNA c. Lambda=temperate (incorporate DNA)

What kinds of enzymes can be found within the virions of RNA viruses? Why are they there?

a. lysozyme i. makes hole in cell wall to allow nucleic acid entry ii. also lyses bacterial cell to release new virions b. neuraminidases i. destroy glycoproteins and glycolipids ii. allows liberation of viruses from cell c. nucleic acid polymerases (RNA replicases: RNA-dependent RNA polymerases) i. RNA replicases: RNA-dependent RNA polymerases ii. Reverse transcriptase: RNA-dependent DNA polymerase in retroviruses

How does attachment contribute to virus-host specificity?

a. major factor in host specificity b. requires complementary receptors on the surface of a susceptible host for its infecting virus c. Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or other cell structures. (Figure 8.11) d. Receptors on host cell carry out normal functions for cell (e.g., uptake proteins, cell-to-cell interaction, flagella, pili).

How is the penetration step in viral replication different in phages and animal viruses? What else would be different in their replication?

a. phages inject and replicate in cytoplasm; animal viruses fuse into the cell and replicate in the nucleus

What is unique about the Pox viruses? What type of damage do they do to their host?

dsDNA, very large, normally lyses b. they replicate in the cytoplasm, which is odd because eukaryotic cells have nuclei, which is where it normally occurs c. herpes virus that can cause cancer???

What disease is associated with coronaviruses?

dsRNA virus b. SARS (Sudden Acute Respiratory Syndrome) 8. What is the shaped and name of the virus that causes rabies? What type of virus is it? a. Rhabdovirus b. Bullet shaped, enveloped, helical nucleocapsid containing several enzymes c. dsRNA virus

What are reoviruses?

dsRNA virus b. respiratory enteric orphan virus c. not associated directly with any specific disease

Compared with cells, what is unusual about viral genomes?

either DNA or RNA genomes b. single-stranded or double-stranded i. Single-stranded may be plus sense (exact same sequence as mRNA) or minus sense (complementary sequence to mRNA). ii. When plus stranded RNA viruses enter the host, translation happens to make more proteins c. either linear or circular d. usually smaller than those of cells

Other Viruses listed in class

ssDNA—Parvovirus (puppies) b. Polio—polio (+RNA) c. Vibrio cholera—cholera, phage that infects a bacteria with a toxin which makes it infect animals