BIOMI 2500: Final (HW)

Caps of host mRNA are cut off by the RNA polymerase of influenza and used as primers of (+) strands destined to be translated (+) strands that are destined to serve as templates for (-) strands (-) strands that are packaged into virions. A and B A, B, and C)

(+) strands destined to be translated

How was "The Berlin Patient" cured of his HIV infection?

- "The Berlin Patient" was an HIV positive person that contracted acute myeloid leukemia and needed bone marrow transplant - Bone marrow donor was homozygous for CCR5delta32 mutation which transferred an immune system to the patient that had no HIV receptors - Patient was permanently cured of virus bc CCR5delta32 mutation made immune cells resistant to HIV

How many mutations are found in the spike protein of Omicron variant BA.5 relative to the Wuhan strain? How many mutations are found in all the other genes combined?

- 30 in spike - 21 in all other proteins combined

Follow this link: "https://ivr.cidrap.umn.edu/universal-influenza-vaccine-technology-landscape" How many recombinant protein vaccines are listed as being in preclinical trials? How many Recombinant Influenza-based trials are listed? How many virus vectored trials? How many trials using virus-like particles? How about the number of trials using non-VLP nanoparticles? How many trials using Nucleic acids? Of all of these strategies, how many are in active phase 3 trials? In no more than 15 words, describe each of the strategies that are in Phase 3 trials.

- 32 recombinant protein vaccines in preclinical, 5 recombinant influenza-based trials, 5 virus vectored trials, 5 virus-like particles, 5 trials using non-VLP nanoparticles, 5 trials nucleic acids - 4 strategies in phase 3: recombinant protein, virus-like particles, non-VLP nanoparticles, nucleic acid. - The recombinant protein vaccine is Multimeric-001 which aims at inducing T cell responses and enhanced B-cell responses to circulating and novel strains. - The virus-like particle vaccine is Quadrivalent VLP which stimulates antibody and cellular immune responses. - The non-VLP nanoparticles vaccine is called Nano-Flu and uses full-length, stabilized recombinant spike proteins. - The nucleic acid vaccines are Modified mRNA lipid nanoparticles and Modified mRNA vaccine which aimed at eliciting robust germinal center and B cell responses.

Describe the "3Q" and "2P" mutations in the spike protein that is used in the Novavax vaccine.

- 3Q alters polybasic cleavage sites so spike protein cannot be cleaved - 2P mutation prevents S2 from unfolding - Together they lock spike protein in a perfusion conformation

What are advantages of measuring biological oxygen demand? What are the disadvantages?

- Advantages: allows researchers to know o2 demand of a sample to improve health of water; doesn't require heating step and is easier than trying to identify each microbe in a sample - Disadvantages: not every microbe is aerobic and some won't contrib to BOD; it takes a lot of time to run; samples could have toxins that prevent microbial activity

Describe the function of aeration tanks that are used in treating sewage. How is the process optimized?

- Aeration tanks will bring h2o and air in close contact by exposing drops of h2o to the air - Aerobic bact growth is supported and breaks down waste - Adding activated sludge causes bacteria to consume the BOD faster

How does alum cause suspended particles to form a sediment?

- Alum is not soluble in water so it stays in its tiny particle form causing particles in the water to flock to it. - They become denser, the sediment forms and it settles. - It can be more easily removed from water.

Describe the two compounds that are included in the antibiotic Augmentin.

- Amoxicillin and clauvanic acid - CA makes irreversible bond w/ beta lactamases (counter defense against enzyme) - Amox interferes w/ transpeptidase

On May 14, 1796, Edward Jenner innoculated the arm of James Phipps with cowpox that had been taken from a pustule on the arm of Sarah Nelmes. On the seventh day, Phipps complained of uneasiness in the axilla. What is an axilla (plural axillae), and why would it become sore? How many days after inoculation was the boy back to full health?

- Axilla is under armpit where lymph nodes are - Inflamed but after day 10, it was ok

If you visit this web site: https://covid.cdc.gov/covid-data-tracker/#variant-proportions you'll find that, as of November 5, the BQ.1.1 variant is the most rapidly expanding SARS-CoV2 variant and may soon displace BA.5 as the most common variant in new infections. What criteria might be used to decide whether to define BQ.1.1 as a new Variant of Concern?

- BQ.1.1 variant is more infectious, more likely to cause breakthrough infections or reinfections in those who are vaccinated or previously infected

Why MUST poliovirus RNA be translated before replication can occur?

- Because poliovirus has a (+) RNA but not the enzyme that produces more RNA - It has to be translated first to replicate more dsRNA.

In doing a Pac-Man PCR, it might seem surprising that the quencher could absorb ALL the fluorescent photons that are released by the fluorophore. Perhaps this might help: How many bases separate the CY5 fluorophore from the BHQ3 quencher? Approximately how many nanometers separate them? How does that compare to the wavelength of visible light?

- Blue light comes onto the Cy5 and it releases green light - The CY5 fluorophore and BHQ3 are placed 20 bases apart which is equivalent to 68 angstroms (3.4 A per 20 bases). 68/10= 6 nm. - Visible light is between 380-700 nm. - large difference between 6 nm and 500 nm means that it covers a big space and likely will absorb the energy.

The CDC claims that in an emergency, water can be made potable by boiling, or by treatment with low amounts of hypochlorite, or by filtration. What sorts of pathogens might escape each of these treatments?

- Boiling, harmful chemicals or toxins cannot be removed - Endospores would survive boiling - Disinfection with hypochlorite it will kill most viruses and bacteria but some strains like S. aureus can escape the treatment; it wouldn't kill endospores

How does the cleavage site of SARS-CoV2 resemble that of the BAT-RaTG13 virus? How does it resemble the cleavage site of the MERS virus?

- Both have spike proteins projecting from virion surface - Both have monobasic cleavage sites - Both have furin

The MARTX family of toxins have a variety of different toxin subunits. However they all have a domain labelled CPD. What is the function of this domain?

- CPD domain is located in all of the MARTX toxins before the start of the C-terminal repeats - Liberates the toxin subunits in the cell membrane. - All toxins have this domain because it must be activated in order for autoproteolysis to occur. CPD domain will bind to molecules that are present in eukaryotic cell cytosol but not in bacteria.

Some clinicians are concerned about the safety of nucleoside analogs such as remdesivir and molnupiravir. What could possibly go wrong?

- Could mutate DNA but they are substrates for RNA synth - Might incorporate into host RNA but only a temporary problem - If large # of mutations occur at DNA level, it could lead to cancer

How do the toxins of enterotoxigenic strains of E. coli resemble those of Vibrio cholerae?

- ETEC contains 2 toxins, heat labile toxin and heat stable toxin. - Heat labile toxin is 80% identical to cholera toxin and the heat stable toxins between ETEC and the vibrio cholerae are also very similar. - The mechanisms of stimulating the opening of the CFTR in both of the toxins are identical as well.

Imagine one person tests positive for anti-Spike IgM while another person tests positive for both anti-spike IgM and anti-spike IgG. What can you conclude about these individuals?

- First person was recently infected - Second person was infected longer time ago

How can vancomycin-resistance genes be transferred between different bacteria? What other genes are also transferred at the same time? Can this transfer occur between different genera bacteria?

- Horizontal gene trasnfer - Require 4 genes: vanX, vanY, vanH, vanA - Transfer to staph

Why is hypochlorite added to Ithaca city water? Shouldn't the filtration step remove all microbes?

- Hypochlorite is needed because filtration removes particles but not insoluble things. - Nutrients feed the biofilms inside of the water pipes so adding hypochlorite removes that. - Hypochlorite is a strong oxidizing agent that kills all microbes left even after filtration. - Some parasites, bacteria, and viruses can still exist in the water even after filtration.

How do the findings of George Soper in 1904 echo those of John Snow fifty years earlier?

- John Snow found that there was a common water hand pump in London that contributed to the spread of cholera. - Similarly, when typhoid was spreading across Ithaca, NY, George Soper found that bodies of water were the sources of the rapid spread of the disease. - Similarly, individuals who contracted typhoid were using a hand pump and also swimming and drinking water from Six mile creek and Buttermilk Falls in Ithaca.

12 of 16 EHEC victims remember eating hamburgers at Jack in the Box within a week of illness onset. What about the other 4 victims? How did they become infected?

- Likely contracted from secondary infections or other sources that sourced meat from same plant

How do Maraviroc and Enfuvirtide inhibit the HIV replication cycle?

- Maraviroc binds to CCR5 protein so that HIV cannot bind - Enfuvirtide blocks formation of the HIV bundle

What is the difference between a microgamont and a microgamete? What role does each play in the infection cycle?

- Microgamonts rupture and release many microgametes which will then fertilize the macrogamonts. - This will produce the unsporulated oocyst which can be passed in the feces to contaminate food/water and infect more people.

Describe the similarities and differences between the methods used by Milwaukee and New York City to remove viable Cryptosporidium oocysts. Do you think these methods would kill endospores?

- NYC chlorinates but didn't filter their water but Milwaukee had an outbreak and they invested $ into UV irradiation at 260 nm to shatter DNA - UV irradiation damages DNA and RNA of microbes - Milwaukee uses an ozone bubbler to purify h2o - In this, ozone gas is bubbled through the h2o to destroy microorgs - Then coagulate is added to form large particles which rise to surface and solids settle - Filtered further to remove small particles, chlorine and fluoride added - Neither would kill endospores

(10/21) In a test of biological oxygen demand, it is necessary to aerate the samples? Is it necessary to leave an air space inside each bottle?

- Necessary to aerate samples so aerobic bact can utilize for work and aeration allows for initial oxygen concentration to be depleted - O2 depletion measured over time - After innoculation, don't want to aerate any longer and don't want air space - If air space exists, it will continue to aerate while oxygen is supposed to be depleted - Test will be invalid because more oxygen will be added

The first SARS-CoV2 variant that appeared is referred to as the alpha variant. What two mutations increased the fitness of this variant?

- New AA in the 3 position in spike trimer to optimize fit b/w spike and ACE2 receptor - Spike P681H mutation, PRRAR sequence altered to HRRAR which enhances cleave of protein by furin

Why is "PBP2a" an odd choice of names for methicillin-resistant transpeptidase of MRSA strains? What is the rationale for this name?

- PBP2a is penicillin-binding protein (transpeptidase) but doesn't bind to penicillin - Reason for this name is because its part of a family of proteins (penicillin binding proteins)

Compare the SARS-CoV2 vaccines made by Pfizer-BioNTech, by AstraZenica-Oxford, and by Novavax. What do they all have in common?

- Pfizer is mRNA vaccine - Astrazeneca is adenovirus that is defective for replication and has a DNA copy of spike gene which causes spike protein synth in APC - Novavax is dsDNA full-length spike protein that introduces 2 mutations (S1/S2 and P2) - All vaccines are vaccines that use SARS-cov-2 spike protein or its genes

Why might the estimate in the previous question require downward revision?

- Possible that there is incomplete data - There may have been a large numbers of asymptomatic infections.`

R-naught is a measure of infectivity of a pathogen. How low must this number be for epidemiologists to conclude that an outbreak will eventually subside?

- R-naught is the # of ppl that an infectious person is likely to infect - If r0 <1, this means disease will fade on its own

Rapid at-home tests for COVID have recently become widely available. Do these tests test for viral RNA, viral protein, or antibodies against the virus? Which tests required sophisticated instuments? Which of them require a blood sample?

- Rapid at-home tests test for antigens like viral proteins - PCR requires more elaborate equp - Antibody requires blood sample

How did manangement at Jack in the Box restaurants initially respond to the outbreak?

- Recalled all meats in the state because procedures left meat pink - Initially weren't going to recall their beef but the press eventually encouraged them too

(11/11) What potential advantages would a nasal vaccine against COVID have compared to a vaccine delivered by syringe?

- Self-administered - Nasal mucosa is 1st barrier so nasal vaccination will induce mucosal and systemic immunity - It stimulates IgA to block binding the virus in the airways - easily accessible

What interventions could cause R-naught to decrease?

- Social distancing - Quarantining - Vaccination - Medications

Describe the origins of two types of Cryptosporidium parasites that can penetrate intestinal epithelial cells.

- Sporozoites come from oocyst - Merozoites come from type 2 miront.

Death rates from all causes combined can be tabulated (slide 113), and excess deaths above the predictions in the past 2.5 years are generally attributed to COVID. What other factors might complicate this conclusion?

- Testing was limited and some COD suppressed - other COD like drug OD, CVD, suicide

How might the HAITIV vaccine protect mice just one day after receiving it. It is possible that Vaxchora might also provide protection after just one day?

- The HaitiV vaccine deleted the diarrheagenic factors and protected against vaccine reversion. - The vaccine produced a probiotic-like protection from cholera. - Enabled an adaptive immunity response allowing the antibodies in the vaccine to be made to neutralize the CxtAB toxin. - Not possible in Vaxchora because this probiotic-like protection is only observed in HaitiV and Vaxchora is the only vaccine licensed in the US. - Additionally, it requires an entire immune response rather than colonizing the gut for protection. - Vaxchora could possibly work this way if it were tested for the probiotic-like protection since it is very similar to the HaitiV vaccine.

What does the headline "Molnupiravir: coding for catastrophe" refer to?

- The drug molnupiravir causes large levels of mutations in the viral genome - Polymerase can still proceed but it makes a large # of mistakes

When PCR was first developed, a temperature-labile DNA polymerase was used. What is the advantage of using a thermostable DNA polymerase? With a temperature-labile polymerase, what extra steps were required?

- The thermostable DNA polymerase allows it to function at high temperatures in order to denature the DNA strands without itself being denatured - With a temperature-labile polymerase, denaturation, anneal and extensions were the additional steps required for DNA amplification:

What is the key feature of tertiary treatment of wastewater? Would the effluent of such treatment be suitable for further purification as potable water?

- Uses anthracite coal and sand like filters - Treated waste even w/o tertiary treatment is used to make potable h2o - If tertiary treated h2o were used as sole source, it might require desalination

What is "variolous matter"? How did the introduction of cowpox virus in Phipp's arm resemble the introduction of variolus matter? Why did this similarity cause Jenner to have "pleasing sensensations"?

- Variolus = affected w/ smallpox but not the full infection - Variolous matter is piece of the virus to be used to inoculate people - Cowpox inoc into arm and had pleasant senses bc lesion bw smallpox and cowpox were similar and could cross-protect

What purposes are served by storing water in elevated towers?

- Water pressure and additional storage time to easily flow through pipes

Excess deaths were detected in the winter of 2018. Were these due to COVID? If not, what might have caused these excess deaths?

- Xs deaths likely not due to COVID but rather a bad influenza outbreak

What do mOPV2 and nOPV2 refer to?

- mOPV2 is monovalent oral polio vaccine 2 aka it is an OPV that only contains mRNA components of one strain of the virus - protects only against wild type 2 - nOPV2 is novel oral polio vaccine 2 -- it is a novel OPV that is able to protect against both wildtype 2 and vaccine derived poliovirus 2 through the unique feature of a "codon deoptimized" capsid protein gene that makes protein synthesis less efficient - this was the vaccine granted by WHO

Describe Moderna's recent trials to develop a vaccine against HIV.

- making them based on HIV proteins and mRNA platform (like covid) - Test on monkeys but will take a few years

(11/4) What was the estimated case fatality rate for 20-29 year olds in mainland China at the beginning of the pandemic?

0.2%

(10/19) Describe two ways that particular genera of bacteria can be detected using fluorescence microscopy.

1. Abs bind to surface antigens unique to cell surfaces 2. FISH: permeabilized cells are fixed to slide and fluorescent probes are released that bind to 16s RNA - Both use fluorescent probs that show up using fluorescence microscopy

How many proteases (or "proteinases") are required to convert the viral polyprotein to mature proteins? How many cleavage sites are shown in the figure on slide 39? 1, 13 2, 13 3, 13 4, 14 2, 12 2, 11 2, 10

2, 13

Mammalian and most mRNA's have a "cap" at their 5' end. Caps consist of an extra G residue fused to the rest of the molecule by a _____ linkage 5'-5' diphosphate 5'-3' diphosphate 3'-5' diphosphate 3'-3' diphosphate 5'-5' triphosphate 5'-3' triphosphate 3'-5' triphosphate 3'-3' triphosphate

5'-5' triphosphate

When hemagglutinin is first synthesized on host ribosomes, it contains (multiple correct answers) A) A signal sequence B) A stop transfer sequence C) A site that will be cleaved by a host protease D) A sequence that will become the "fusion peptide" E) None of the above.

A) A signal sequence B) A stop transfer sequence C) A site that will be cleaved by a host protease D) A sequence that will become the "fusion peptide"

When the spike protein of HIV is first synthesized on host ribosomes, it contains (multiple correct answers) A) A signal sequence B) A stop transfer sequence C) A site that will be cleaved by a host protease D) A sequence that will become the "fusion peptide" E) A domain that will bind to CD4 and CCR5 F) None of the above.

A) A signal sequence B) A stop transfer sequence C) A site that will be cleaved by a host protease D) A sequence that will become the "fusion peptide" E) A domain that will bind to CD4 and CCR5

What functions in the SARS life cycle are carried out by the Spike protein? (Multiple correct answers) A) Adhesion to the host receptor angiotensin converting enzyme (ACE2) B) Adhesion to angiotensin C) Fusion of the viral envelope to the mitochondrial membrane D) Synthesis of a 5' Cap E) Synthesis of a poly-A tail F) Fusion of the viral envelope with the endosomal membrane

A) Adhesion to the host receptor angiotensin converting enzyme (ACE2) F) Fusion of the viral envelope with the endosomal membrane

To make an RNA vaccine against SARS-CoV2, one must (multiple correct answers) A) Assemble the full length spike protein from synthetic DNA fragments B) Clone the gene into a bacterial plasmid adjacent to a strong promoter C) Introduce the recombinant plasmid into bacteria for propagation D) Purify the plasmid DNA E) To the plasmid DNA, add RNA polymerase and substrates for mRNA F) Purify the mRNA G) Encase mRNA in a lipid nanodrop H) Place a drop of vaccine on a sugar cube for oral administration.

A) Assemble the full length spike protein from synthetic DNA fragments B) Clone the gene into a bacterial plasmid adjacent to a strong promoter C) Introduce the recombinant plasmid into bacteria for propagation D) Purify the plasmid DNA E) To the plasmid DNA, add RNA polymerase and substrates for mRNA F) Purify the mRNA G) Encase mRNA in a lipid nanodrop

Poliovirus inhibits the synthesis of host proteins by (multiple correct answers) A) Destroying proteins that are required for CAP-dependent translation initiation B) Destroying host Capping enzymes C) Destroying host mRNA D) Destroying host DNA E) Destroying host ribosomes. F) Blocking the function of nuclear pores that normally allow host mRNA to enter the cytoplasm

A) Destroying proteins that are required for CAP-dependent translation initiation F) Blocking the function of nuclear pores that normally allow host mRNA to enter the cytoplasm

Which of the following strategies are used by bacteria to resist the lethal effects of various antibiotics? (multiple correct answers) A) Exporting the antibiotic through a dedicated export permease B) Covalently altering the antibiotic by addition of the methyl group, an acetate group, or another modification C) Destroying the antibiotic by hydrolysis D) Replacing the target of the antibiotic with a protein having a similar function but which is resistant to the antibiotic E) Point mutation of a chromosomal gene that alters the target or decreases envelope permeability.

A) Exporting the antibiotic through a dedicated export permease B) Covalently altering the antibiotic by addition of the methyl group, an acetate group, or another modification C) Destroying the antibiotic by hydrolysis D) Replacing the target of the antibiotic with a protein having a similar function but which is resistant to the antibiotic E) Point mutation of a chromosomal gene that alters the target or decreases envelope permeability.

In determining whether a person is infected by HIV, one could test for (multiple correct answers) A) HIV RNA in plasma B) HIV proviral DNA in PBMCs (peripheral blood mononuclear cells) C) HIV proteins D) Anti-HIV IgM E) Anti-HIV IgG

A) HIV RNA in plasma B) HIV proviral DNA in PBMCs (peripheral blood mononuclear cells) C) HIV proteins D) Anti-HIV IgM E) Anti-HIV IgG

Of the following, which is detectable earliest? Which would be detectable last? (multiple correct answers) A) HIV RNA in plasma B) HIV proviral DNA in PBMCs (peripheral blood mononuclear cells, also known as monocytes) C) HIV proteins D) Anti-HIV IgM E) Anti-HIV IgG

A) HIV RNA in plasma E) Anti-HIV IgG

Zidovudine (multiple correct answers) A) Has a nitrogenous base identical to thymine B) Has a 2' OH group C) Has an N3 (azide) group at the 3' position. D) Has a triphosphate at the 5' position E) Is a substrate for cellular enzymes that can add the triphosphate at the 5' position.

A) Has a nitrogenous base identical to thymine C) Has an N3 (azide) group at the 3' position. E) Is a substrate for cellular enzymes that can add the triphosphate at the 5' position.

Nucleoside analog reverse transcriptase inhibitors (multiple correct answers) A) Have a nitrogenous base identical or similar to adenine, guanine, cytosine, or thymine B) Are converted to a triphosphate by host cells C) Can be incorporated by reverse transcriptase into a growing DNA polymer D) Have a deoxyribose analog that is incompatible with further chain elongation E) Can be removed from the DNA polymer by the RNase H activity of Reverse Transcriptase.

A) Have a nitrogenous base identical or similar to adenine, guanine, cytosine, or thymine B) Are converted to a triphosphate by host cells C) Can be incorporated by reverse transcriptase into a growing DNA polymer D) Have a deoxyribose analog that is incompatible with further chain elongation

Which Influenza proteins are found at least partly on the surface of the virus particle? A) Hemagglutinin B) Matrix C) M2 D) Neuraminidase E) NP F) NS1 G) NEP H) Polymerase acidic I) Polymerase basic 1 J) Polymerase basic 2

A) Hemagglutinin C) M2 D) Neuraminidase

The fact that the H5N1 influenza virus binds preferentially to 2-3 sialic acids makes the H5N1 bind only in the lower respiratory tract of humans, making these viruses (multiple correct answers) A) Highly lethal but poorly contagious B) Seldom lethal but poorly contagious C) Highly lethal and highly contagious D) Seldom lethal and highly contagious E) Evolvable by antigenic drift to a highly lethal and highly contagious form that binds both 2-3 and 2-6 sialic acids.

A) Highly lethal but poorly contagious E) Evolvable by antigenic drift to a highly lethal and highly contagious form that binds both 2-3 and 2-6 sialic acids.

Negative DNA supercoiling is useful because (multiple correct answers) A) It helps particular regions of DNA to "melt" i.e. to become single-stranded, especially those regions that are rich in A:T base pairs. B) it holds together the antiparallel strands of DNA in the double helix. C) it provides energy for transcription. D) it prevents RNA from pairing with DNA in the double helix. E) It helps to make a chromosome more compact.

A) It helps particular regions of DNA to "melt" i.e. to become single-stranded, especially those regions that are rich in A:T base pairs. E) It helps to make a chromosome more compact.

Which of the following statements about HIV integrase are correct (multiple correct answers) A) It is encoded by HIV B) It is found in the shorter of the two polyproteins C) Its proteolytic activity is present even before it has excised from its polyprotein. D) It causes HIV integration as a specific site of the human genome. E) It can mediate excision from the genome.

A) It is encoded by HIV C) Its proteolytic activity is present even before it has excised from its polyprotein.

Which of the following proteins is created by digestion by HIV protease (multiple correct answers)? A) MA B) CA C) NC D) PR E) RT F) IN G) SU H) TM

A) MA B) CA C) NC D) PR E) RT F) IN

Which class of HIV antivirals is sold under the name Dovato? (multiple correct answers) A) Nucleoside Analog RT inhibiters B) Non-nucleoside analog RT inhibitors C) Protease Inhibitors D) Integrase Inhibitors E) CCR5 inhibitors F) TM inhibitors

A) Nucleoside Analog RT inhibiters D) Integrase Inhibitors

Which of the following statements about coronavirus protein expression is accurate? (multiple correct answers) A) Some ribosomes that start synthesizing protein at "ns1" synthesize a polyprotein whose digestion yields approximately 10 mature proteins B) Some ribosomes that start synthesizing protein at "ns1" make a longer polyprotein whose digestion yields approximately 15 mature proteins. C) This longer polyprotein requires a -1 frameshift in the translation of the mRNA. D) This -1 frameshift occurs directly upstream of the RdRp gene. E) This frameshift requires a folded mRNA structure called a "pseudoknot" in the mRNA directly downstream of the frameshift. F) This frameshift ensures that more RdRp (RNA dependent RNA polymerase) is synthesized than either of the two proteases.

A) Some ribosomes that start synthesizing protein at "ns1" synthesize a polyprotein whose digestion yields approximately 10 mature proteins B) Some ribosomes that start synthesizing protein at "ns1" make a longer polyprotein whose digestion yields approximately 15 mature proteins. C) This longer polyprotein requires a -1 frameshift in the translation of the mRNA. D) This -1 frameshift occurs directly upstream of the RdRp gene. E) This frameshift requires a folded mRNA structure called a "pseudoknot" in the mRNA directly downstream of the frameshift.

(10/14) Reverse transcriptase (multiple correct answers) A) Synthesizes DNA B) Synthesizes RNA C) If provided with a (+) stranded molecule, will synthesize the (-) strand D) If provided with a (+) stranded molecule, will synthesize the (+) strand E) Requires rNTPs for substrates F) Requires dNTPs for substrates. G) Generates pyrophosphate as a side product.

A) Synthesizes DNA C) If provided with a (+) stranded molecule, will synthesize the (-) strand F) Requires dNTPs for substrates. G) Generates pyrophosphate as a side product.

Which of the following steps is required for bacteria to become resistant to vancomycin (multiple correct answers) A) They must hydrolyze D-ala-D-ala dipeptide B) They must hydrolyze D-ala from the pentapeptide C) They must overproduce D-lactate, using pyruvate as a substrate D) They must synthesize D-ala-D-lactate E) They must use a "housekeeping" enzyme to join the L-Ala-D-glu-L-Lys tripeptide to the D-ala-D-lactate

A) They must hydrolyze D-ala-D-ala dipeptide B) They must hydrolyze D-ala from the pentapeptide C) They must overproduce D-lactate, using pyruvate as a substrate D) They must synthesize D-ala-D-lactate E) They must use a "housekeeping" enzyme to join the L-Ala-D-glu-L-Lys tripeptide to the D-ala-D-lactate

Which of the following has been used to suppress overactive immune systems? (multiple correct answers) A) Tocilizumab B) Nirmatrelvir C) Ebselen D) Remdesivir E) Dexamethasone F) Ritonavir

A) Tocilizumab E) Dexamethasone

(11/18) At least one isolate of the 1918 influenza virus was able to bind both alpha2-3 and alpha2-6 sialic acids. Binding alpha2-3 sialic acids may have caused ____ resulting in _____, while binding alpha2-6 sialic acids may have caused _____, resulting in ______ A. Binding to cells deep in the lung/ life-threatening infections/ binding to cells in the upper respiratory tract/ high levels of contagion. B. Binding to cells in the upper respiratory tract/ life-threatening infections/ binding to cells deep in the lung/ high levels of contagion. C. Binding to cells deep in the lung/ high levels of contagion/ binding to cells in the upper respiratory tract/ life-threatening infections. D. Binding to binding to cells in the upper respiratory tract/ high levels of contagion/ cells deep in the lung/ life-threatening infections.

A. Binding to cells deep in the lung/ life-threatening infections/ binding to cells in the upper respiratory tract/ high levels of contagion.

How many single-stranded DNA fragments would be made in N cycles per input molecule if just one oligonucleotide primer were added rather than two? A. N B. 2N C. 2^N D. 10N E. N2 F. N! (N factorial)

A. N

(9/30) The processing of cholera toxin into 2 protein fragments that are held together by a disulfide bond is reminiscent of (circle all correct answers) A. Shiga toxin. B. Exotoxin A C. Heat-Labile toxin (LT) D. Tetanus toxin E. Botulism toxin F. Heat-Stable toxin (ST) of ETEC.

A. Shiga toxin. B. Exotoxin A C. Heat-Labile toxin (LT) D. Tetanus toxin E. Botulism toxin

What factors caused the pandemic to end abruptly in 1919? (multiple correct answers) A) Many had survived an infection and had strong immunity B) Those with strong immunity protected their neighbors by herd immunity C) Immune mothers may have protected their infants by donating maternal antibodies against influenza D) The viruses evolved to a more benign form. E) Cessation of hostilities

All A) Many had survived an infection and had strong immunity B) Those with strong immunity protected their neighbors by herd immunity C) Immune mothers may have protected their infants by donating maternal antibodies against influenza D) The viruses evolved to a more benign form. E) Cessation of hostilities

Which of the following factors contributed to the "favorable environment" that caused a single case of HIV infection to spread in the early 20th century in or near Kinshasa, formerly Leopoldville? (multiple correct answers) A) Rapid industrialization B) Forced labor in large labor camps C) Displacement D) Urbanization E) Population increase F) Prostitution G) Disease, malnutrition H) Unsterile injection of vaccines and antibiotics.

All A) Rapid industrialization B) Forced labor in large labor camps C) Displacement D) Urbanization E) Population increase F) Prostitution G) Disease, malnutrition H) Unsterile injection of vaccines and antibiotics.

Which RNA strands are identical in all vaccine strains? None All but H and N All but H All but N All but H, N, and M All but H, N and PB

All but H and N

In 2009, a new influenza virus appeared and evolved by antigenic shift. Its eight fragments can ultimately be traced back to H1N1 Eurasian "Avian-like" swine virus H1N1 Classical swine virus H1N1 Avian virus H3N2 seasonal human virus A and C B and D A, B and D All of the above.

All of the above.

Influenza virus has a high rate of __ because its ___ lacks ____ Antigenic shift; RNA replicase; exonuclease activity Antigenic shift; DNA replicase, endonuclease activity Antigenic drift; DNA replicase; exonuclease activity Antigenic drift; RNA replicase; exonuclease activity Antigenic drift; RNA replicase; endonuclease activity

Antigenic drift; RNA replicase; exonuclease activity

Oral polio vaccine (multiple correct answers) A) Was developed by Jonas Salk, who had a lifelong antipathy toward Albert Sabin. B) Consists of a live attenuated polio virus with an adenine residue at position 480 altered to a guanine. C) Mimics a polio infection better than the earlier vaccine and therefore is more effective. D) Can mutate back to the original fully virulent polio strain E) Is responsible for a small number of cases of circulating vaccine-derived paralytic polio (cVDPP). F) Is responsible for the elimination of wild type polio from all but a few countries.

B) Consists of a live attenuated polio virus with an adenine residue at position 480 altered to a guanine. C) Mimics a polio infection better than the earlier vaccine and therefore is more effective. D) Can mutate back to the original fully virulent polio strain E) Is responsible for a small number of cases of circulating vaccine-derived paralytic polio (cVDPP). F) Is responsible for the elimination of wild type polio from all but a few countries.

Nucleoside Analog DNA synthesis inhibitors (Multiple correct answers) A) Must have an OH group at the 3' position of the deoxyribose B) Could have an H group at the 3' position of the deoxyribose C) Could have an N3 (azide) group at the 3' position of the deoxyribose D) Could have a double bond between the 2' and 3' positions of the deoxyribose E) Could lack the 2' and 3' carbons of the deoxyribose

B) Could have an H group at the 3' position of the deoxyribose C) Could have an N3 (azide) group at the 3' position of the deoxyribose D) Could have a double bond between the 2' and 3' positions of the deoxyribose E) Could lack the 2' and 3' carbons of the deoxyribose

Which nucleobases can form hydrogen bonds with remedisivir? A) A B) G C) C D) U

B) G C) C D) U

All humans, including archaic humans, express a type of sialic acid called Neu5Ac, while great apes and other animals express a similar sialic acid called Neu5Gc, which is created from Neu5Ac by hydroxylation. Humans have a deletion of part of the gene encoding the hydroxylase. This mutation might plausibly have caused resistance to an unknown virus or toxin. If so, which of the following has co-evolved to bind to the human form of sialic acid? A) Shiga toxin B) Influenza virus C) Diphtheria toxin D) Cholera toxin E) Typhoid toxin.

B) Influenza virus E) Typhoid toxin.

Poliovirus (multiple correct answers) A) Is enveloped B) Is naked C) Has (+) stranded nucleic acid D) Has (-) stranded nucleic acid E) Virion contains RNA. G) Virus infection cycle closely resembles that of Rhinovirus I) Has one nucleic acid strand per virion J) Has multiple nucleic acids strands per virion

B) Is naked C) Has (+) stranded nucleic acid E) Virion contains RNA. G) Virus infection cycle closely resembles that of Rhinovirus I) Has one nucleic acid strand per virion

All Influenza viruses (multiple correct answers) A) Packages DNA in its virion B) Packages RNA in its virion C) Packages (+) stranded nucleic acid in its virion D) Packages (-) stranded nucleic acid in its virion E) Packages double-stranded nucleic acid in its virion.

B) Packages RNA in its virion D) Packages (-) stranded nucleic acid in its virion

Typhoid toxin has enzymatic activities similar to those of A) Cholera toxin B) Pertussis toxin C) Shiga toxin D) Cytolethal distending toxin E) Exotoxin A F) Diphtheria toxin G) Endotoxin

B) Pertussis toxin D) Cytolethal distending toxin

When influenza viruses enter endosomes of host cells, the acidic pH causes (multiple correct answers) A) Proteolysis of hemagglutinin B) Release of the sialic acid binding domain of hemagglutinin C) The conversion of two shorter alpha helices into one long alpha helix D) Exposure a previously buried fusion peptide to the endosomal membrane E) The conversion of monomers of hemagglutinin into trimers.

B) Release of the sialic acid binding domain of hemagglutinin C) The conversion of two shorter alpha helices into one long alpha helix D) Exposure a previously buried fusion peptide to the endosomal membrane

Which of the following bacteria were inhibited by the original preparations of penicillin? (multiple correct answers) A) B coli (now Escerichia coli) B) Staphylococcus C) Streptococcus D) Pneumococcus E) Gonococcus F) B diphtheriae (now Corynebacterium diphtheriae) G) B influenza (now Haemophilus influenzae)

B) Staphylococcus C) Streptococcus D) Pneumococcus E) Gonococcus F) B diphtheriae (now Corynebacterium diphtheriae)

Reverse transcriptase of HIV (multiple correct answers) A) Synthesizes RNA B) Synthesizes DNA C) Synthesizes single-stranded and double-stranded nucleic acid D) Requires a tRNA primer E) Requires an rRNA primer F) Can degrade RNA in an RNA-DNA duplex G) Can degrade DNA in an RNA-DNA duplex

B) Synthesizes DNA C) Synthesizes single-stranded and double-stranded nucleic acid D) Requires a tRNA primer F) Can degrade RNA in an RNA-DNA duplex

Which of the following statements about the Spike protein are accurate? (multiple correct answers) A) Four Spike submits bind together to form a tetramer. B) When first synthesized Spike has an "SP" sequence that initiates protein secretion. This SP sequence is removed during or after protein secretion. C) Spike has a "TM" sequence that stops secretion so that mature Spike spans the viral envelope. D) Approximately 40 amino acids of spike remain in the inside of the virus particle, while the rest lies in the membrane or outside the virus

B) When first synthesized Spike has an "SP" sequence that initiates protein secretion. This SP sequence is removed during or after protein secretion. C) Spike has a "TM" sequence that stops secretion so that mature Spike spans the viral envelope. D) Approximately 40 amino acids of spike remain in the inside of the virus particle, while the rest lies in the membrane or outside the virus

All of the following are true of HIV except? A. It jumped from apes and monkeys to humans at least six different times B. SIV sequences from gorillas most closely resemble HIV 1/M, which is the pandemic lineage. C. The jump to humans is most likely through butchering or consumption of wild game. D. It probably originated in or near what is now the Democratic Republic of the Congo E. HIV viral load slowly increases inside infected humans

B. SIV sequences from gorillas most closely resemble HIV 1/M, which is the pandemic lineage.

Vancomycin blocks cell wall synthesis by Making a covalent bond with transpeptidase Blocking alanine racemase Binding tightly to the last two amino acids of the pentapeptide Binding to the two phosphates that are bound to bactoprenol. Making pores in the membrane that depolarize it.

Binding tightly to the last two amino acids of the pentapeptide

What BOD is really measuring?

Biodegradable compounds in the sample

Cycloserine blocks cell wall synthesis by Making a covalent bond with transpeptidase Blocking alanine racemase and D-alanine ligase Binding tightly to the last two amino acids of the pentapeptide Binding to the two phosphates that are bound to bactoprenol. Making pores in the membrane that depolarize it.

Blocking alanine racemase and D-alanine ligase

How are the nine or so proteins of HIV expressed? (multiple correct answers) A) Each is encoded by a separate RNA, as found in influenza virus B) Each is synthesized as a separate mRNA, as found in ebola and measles viruses C) Each is synthesized by alternative splicing of an RNA D) In some cases, mature proteins are made by proteolysis of a polyprotein by HIV protease E) In one case, two mature proteins are made by proteolysis of a polyprotein by the host protease furin

C) Each is synthesized by alternative splicing of an RNA D) In some cases, mature proteins are made by proteolysis of a polyprotein by HIV protease E) In one case, two mature proteins are made by proteolysis of a polyprotein by the host protease furin

Influenza virus (multiple correct answers) A) Is icosahedral B) Is filamentous C) Is sometimes referred to as pleomorphic D) Has an RNA genome E) Has a double-stranded genome F) Has a positive-stranded genome G) Has a lipid envelope H) Has Neuraminidase and Hemagglutinin proteins on its surface

C) Is sometimes referred to as pleomorphic D) Has an RNA genome G) Has a lipid envelope H) Has Neuraminidase and Hemagglutinin proteins on its surface

The 4th generation test for HIV can detect (multiple correct answers). A) HIV RNA B) HIV proviral DNA C) P24 antigen D) Anti-IgM antibodies E) Anti-IgG antibodies F) Abundance of CD4 cells. G) Anti-HIV antibodies.

C) P24 antigen G) Anti-HIV antibodies.

Synthesis of the longer gag-pol polyprotein rather than the shorter gag polyprotein (multiple correct answers) A) Requires slippage of reverse transcriptase during a run of U residues B) Requires slippage of RNA polymerase during a run of U residues C) Requires slippage of a ribosome during a run of U residues D) Occurs about 5% of the time, ensuring a ratio of 1 gag-pol polyproteins per 19 gag polyproteins E) Occurs about 5% of the time, ensuring a ratio of 1 gag polyproteins per 19 gag-pol polyproteins

C) Requires slippage of a ribosome during a run of U residues D) Occurs about 5% of the time, ensuring a ratio of 1 gag-pol polyproteins per 19 gag polyproteins

If a PCR reaction were carried out for N cycles and no reagents were depleted, how many DNA fragments could be created per input DNA? A. N B. 2N C. 2^N (2 raised to the power of N) D. 10N E. N2 F. N! (N factorial)

C. 2^N (2 raised to the power of N)

How does HIV manage to synthesize 20-fold more MA, CA, and NP proteins than PR, RT, and IN proteins? A. When converting RNA to DNA, 5% of reverse transcriptase molecules slip 1 nucleotide at a run of U residues, creating in a new reading frame that encodes the MA, CA, NP, PR, RT, and IN proteins. B. When converting RNA to DNA, 5% of reverse transcriptase molecules fail to synthesize the DNA that encodes the PR, RT, and IN proteins. C. When translating the MA, CA, and NP polyprotein, 5% of the ribosomes slip 1 nucleotide at a run of U residues, and continue in a new reading frame to synthesize the PR, RT, and IN proteins. D. When transcribing HIV proviral DNA, 5% of host RNA polymerase molecules slip 1 nucleotide at a run of U residues, creating in a new reading frame that encodes the MA, CA, NP, PR, RT, and IN proteins. E. 5% of mRNAs are unspliced and synthesize MA, CA, NP, PR, RT, and IN, while 95% are spliced in such a way that PR, RT, and IN sequences are removed.

C. When translating the MA, CA, and NP polyprotein, 5% of the ribosomes slip 1 nucleotide at a run of U residues, and continue in a new reading frame to synthesize the PR, RT, and IN proteins.

Which monoclonal antibodies are effective against both the Wuhan strain and the B.1.1.529 variant? (slide 78)

COV-2196, COV-2130, and S309

Synthesis of poliovirus proteins requires mRNA that (multiple correct answers) A) Has a Cap (an extra G added to the 5' end of the RNA) made by the viral L protein B) Has a Cap that is made by host capping enzymes C) Has a Cap that is "snatched" from host mRNA's D) Has an IRES and no cap. E) Has a long poly-A tail

D) Has an IRES and no cap. E) Has a long poly-A tail

Which of the following proteins are synthesized on ribosomes that are associated with the endoplasmic reticulum? (multiple correct answers) A) PB1 (RNA polymerase basic 1) B) PB2 (RNA polymerase basic 2) C) PA (RNA polymerase acidic) D) NA (Neuraminidase) E) HA (Hemagglutinin) F) M1 (Matrix protein 1) G) M2 (Matrix protein 2) H) NP (Nucleocapsid protein) I) NS1 (Nonstructural proteion 1) J) NS2 (Nonstructural protein 2)

D) NA (Neuraminidase) E) HA (Hemagglutinin) G) M2 (Matrix protein 2)

Clinicians can determine the nucleic acid sequence of a patient's HIV to help them prescribe the optimal antiviral medications. When doing so, which two genes are sequenced? (multiple correct answers) A) MA B) CA C) NC D) Protease E) Reverse Transcriptase F) Integrase G) Surface (component of the spike) H) Transmembrane (component of the spike) I) Tat J) Nef K) Vif L) Vpr M) Vpu

D) Protease E) Reverse Transcriptase

(10/12) Typhoid toxin has A. 5 identical B subunits and 1 A subunit B. 5 dissimilar B subunits and 1 A subunit C. 5 identical B subunits and 2 identical A subunits D. 5 identical B subunits and 2 dissimilar A subunits.

D. 5 identical B subunits and 2 dissimilar A subunits.

Amantadine blocks the acidification of the ___, preventing __ A. Endosome, hemagglutinin-mediated membrane fusion B. Endosome, viral uncoating C. Virion interior, hemagglutinin-mediated membrane fusion D. Virion interior, viral uncoating E. Removal of sialic acid by neuraminidase

D. Virion interior, viral uncoating

Ciprofloxacin and Levofloxacin target Ribosomes DNA polymerases DNA gyrase RNA polymerases Transglycosylases

DNA gyrase

Beta-lactamase acts by Modifying penicillin by methylation (addition of a CH3 group) Pumping penicillin out of the cell. Replacing the target of penicillin with a functionally similar protein. Destroying penicillin by hydrolysis. Removing penicillin from the active site of the transpeptidase, restoring the protein to a functional form.

Destroying penicillin by hydrolysis.

Which MAMP might the virus release during infection? Peptidoglycan Lipopolysaccharide Flagellin Double-stranded DNA Double-stranded RNA Formyl-Met-peptides

Double-stranded RNA

Circulating Vaccine-derived Polio Type 2 was eradicated worldwide in A. 2010 B. 2012 C. 2014 D. 2016 E. none of the above.

E. none of the above. (eradicated in 2015)

Wild type Polio Type 1 was eradicated worldwide in A. 2010 B. 2012 C. 2014 D. 2016 E. none of the above.

E. none of the above. (still low levels in Pakistan and Afghanistan)

Which of the following are being tested as a possible vaccine for COVID? (multiple correct answers) A) Whole viable SARS-CoV-2 B) The SARS virus from 2003 C) MERS virus D) Coronaviruses that cause common colds E) Adenoviruses F) Adenoviruses that have a copy of the gene encoding Spike G) SARS Lipopolysaccharide H) SARS-CoV-2 ribosomal RNA I) mRNA encoding Spike, encapsulated within a lipid nanoparticle

F) Adenoviruses that have a copy of the gene encoding Spike I) mRNA encoding Spike, encapsulated within a lipid nanoparticle

PltB subunits form a pentamer that resemble A. Subunits S2 and S3 of the heat-labile toxin B. Subunits S2 and S3 of the heat-stable toxin C. Subunits S2 and S3 of adenylate cyclase toxin D. The StxA subunit of shiga toxin E. The StxB subunit of shiga toxin F. None of the above

F. None of the above (It is similar to S2 and S3 of pertussis)

The 1918 Spanish Flu and the 2009 Swine flu both were of the ______ serotype. H1N1 H2N2 H3N2 H5N1 H7N7

H1N1

People who were 88 years old in 1918 had been exposed to the __ as children and were ______ protected against the Spanish Flu pandemic. H1N1, strongly H1N8, partially H3N8, poorly H1N1, partially H1N8, poorly None of the above

H1N1, strongly

People who were 68 years old in 1918 had been exposed to the __ as children and were ______ protected against the Spanish Flu pandemic. H1N1, strongly H1N8, partially H3N8, poorly H1N1, partially H1N8, poorly

H1N8, partially

The antivirals Zanamivir and Oseltamivir resemble sialic acid and bind to the active site of neuraminidase. It should in principle be possible to develop other drugs that resemble sialic acid and bind to Hemagluttinin RNA-dependent RNA polymerase Ion channel (M2) Matrix protein (M1) Nucleoprotein (NP)

Hemagluttinin

The mecA gene of MRSA strains encodes a protein that Hydrolyzes penicillin-type antibiotics Alters the penta-peptide to L-ala-D-glu-L-Lys-D-ala-D-ala to L-ala-D-glu-L-Lys-D-ala-D-lactate Is resistant to clavulanic acid Is a penicillin-resistant transpeptidase Detects vancomycin.

Is a penicillin-resistant transpeptidase

Penicillin and carbapenems and cephalosporins block cell wall synthesis by Making a covalent bond with transpeptidase Blocking alanine racemase Binding tightly to the last two amino acids of the pentapeptide Binding to the two phosphates of bactoprenol. Making pores in the membrane that depolarize it.

Making a covalent bond with transpeptidase

Which four countries have had recent (September 2022) cases of wild type Polio Type 1?

Malawi, Pakistan, Afghanistan, Mozambique

How many strains of coronavirus are recognized as human pathogens? How many were known to be deadly prior to the year 2000? 5, 1 6, 0 7, 1 8, 0 9, 1 None of the above

None of the above

Influenza virus contains ___ RNA particles and encodes ___ proteins 1, 6 2, 7 3, 8 5, 9 7, 10 9, 10 None of the above

None of the above

Variola virus is the causative agent of smallpox. "Variolation" refers to the practice of immunizing patients against smallpox using Variola virus that had been rendered safe by Treatment with formaldehyde Treatment with carbolic acid Treatment with high temperature Attenuation by growth in culture for many generations None of the above

None of the above

Which class of HIV antivirals is sold under the name Truvada for the prevention of HIV infection in high-risk populations? Nucleoside Analog RT inhibiters Non-nucleoside analog RT inhibitors Protease Inhibitors Integrase Inhibitors CCR5 inhibitors TM inhibitors

Nucleoside Analog RT inhibiters

The Coronavirus infection cycle requires a DNA-dependent DNA polymerase DNA-dependent RNA polymerase RNA-dependent DNA polymerase RNA-dependent RNA polymerase

RNA-dependent RNA polymerase

Which of the following antibiotics targets RNA polymerase? Streptomycin Rifamycin Tetracycline Chloramphenicol Erythromycin

Rifamycin

Contamination of which water source was responsible for the 1903 outbreak of typhoid fever that caused the death of 1% of all Cornell students?

Six Mile Creek

What evidence is NOT cited as evidence that Abraham Lincoln was suffering from smallpox as he gave the Gettysburg Address? Lincoln reported weakness on the morning that he gave the address A red rash appeared on the fourth day of symptoms that developed into scatter blisters Lincoln's son Tad was earlier diagnosed with a fever and rash. Lincoln's physician made a diagnosis of smallpox. Lincoln was bedridden for approximately 2 weeks after symptoms appeared. Full recovery required approximately 7 weeks. Lincoln's personal valet died of smallpox a few weeks after Lincoln's illness appeared Smallpox scars are visible on photographs of Lincoln.

Smallpox scars are visible on photographs of Lincoln.

Which of the following statements about the Spike protein is correct? The N-terminal half of the protein contains a "fusion peptide" (FP) that is embedded in the endosome membrane, leading to fusion of the viral envelope with the endosome. Spike is cleaved by host proteases at residue 679 Spike is cleaved by viral proteases at residue 679 The C-terminal half of the protein binds the ACE2 host receptor.

Spike is cleaved by host proteases at residue 679

Which of the following antibiotics targets the protein synthesis apparatus? Streptomycin Penicillin Levofloxicin Cycloserine Rifamycin

Streptomycin

Based on the previous question, you might predict that people who survived the 1918 epidemic as young children would likely be ______ protected against the 2009 swine flu epidemic. (The correct answer has been confirmed). Strongly Partially Poorly Not

Strongly

The poly-A tails of influenza mRNA are Obtained by tail-snatching Obtained by Cap-snatching Synthesized by viral RNA polymerase from an equivalent number of U residues on the (-) strands Synthesized by slippage of viral RNA polymerase during the transcription of a short run of U residues on the (-) strands.

Synthesized by slippage of viral RNA polymerase during the transcription of a short run of U residues on the (-) strands.

(12/2) How is it that some humans are naturally resistant to HIV? They are heterozygous for CCR5 loss of function mutations They are homozygous for CCR5 They are homozygous for CCR5 loss of function mutations They are heterozygous for CXCR4 loss of function mutations They are homozygous for CXCR4 They are homozygous for CXCR4 loss of function mutations Both A and B Both A and C

They are homozygous for CCR5 loss of function mutations

Which of the following are required for whole-genome sequencing using the Oxford Nanopore technology (multiple correct answers)? a) A membrane that blocks electrical current. b) The four nucleotide substrates for DNA synthesis with fluorescent tags attached to each purine or pyrimidine. c) An apparatus containing thousands of zero mode waveguides (ZMW) that have glass bottoms to allow illumination by a laser. d) A agarose gel box with six electrodes arranged in a hexagon. e) A heat-stable DNA polymerase. f) A helicase enzyme g) A protein pore

a) A membrane that blocks electrical current. f) A helicase enzyme g) A protein pore

(10/26) Which of the following are required to carry out pulse field gel electrophoresis (multiple correct answers)? a) A protease such as proteinase K (perhaps some lysozyme wouldn't hurt) b) An exonuclease c) An agarose gel apparatus with two opposing electrodes d) A power supply e) An apparatus to form agarose plugs containing whole bacterial cells. f) DNA molecular weight standards between 1 and 10 kilobases g) A restriction endonuclease that cuts bacterial genomes at six-base sequences, generating a thousand DNA fragments. h) Software to digitize and compare fingerprints from different laboratories.

a) A protease such as proteinase K (perhaps some lysozyme wouldn't hurt) d) A power supply e) An apparatus to form agarose plugs containing whole bacterial cells. h) Software to digitize and compare fingerprints from different laboratories.

Which of the following is true of SARS-CoV2 (multiple correct answers) a) Enveloped b) filamentous c) Spike protein forms a tetramer that functions as an adhesin d) Genome is made of DNA e) Genomes are double-stranded f) Genomes are (-) stranded g) Genomes are approximately 30 kilobases in length.

a) Enveloped g) Genomes are approximately 30 kilobases in length.

Use of REGN-CoV2 antibodies is an example of Natural Active Immunity Natural Passive Immunity Artificial Active Immunity Artificial Passive Immunity

artificial passive immunity

Which of the following are required for whole-genome sequencing using the PacBio technology? a) A protein pore b) The four nucleotide substrates for DNA synthesis with fluorescent tags attached directly to each purine or pyrimidine. c) An apparatus containing thousands of zero mode waveguides (ZMW) that have glass bottoms to allow illumination by a laser. d) A heat-stable DNA polymerase. e) A agarose gel box with six electrodes arranged in a hexagon. f) A helicase enzyme g) An exonuclease h) A membrane that blocks electrical current.

c) An apparatus containing thousands of zero mode waveguides (ZMW) that have glass bottoms to allow illumination by a laser.

The Crispr/Cas9 system is currently being evaluated as an agent in combatting HIV. One strategy is to use virus-like particles that resemble HIV and have the same adhesins to deliver the genes encoding Crispr/Cas9 to cells that are targeted by HIV. These virus-like particles would contain nucleic acids that encode Crispr/Cas9 complexes. Such CRISPR-Cas9 complexes could possibly _______ infections by targeting ________, or might help to _________ infections by targeting ______ Manage or cure / HIV integrase enzyme / prevent / reverse transcriptase enzyme prevent / proviral DNA / Manage or cure / HIV protease enzyme prevent / HIV viral RNA / manage or cure / HIV integrase enzyme prevent / CCR5 gene / manage or cure / HIV proviral DNA. Manage or cure / CCR5 gene / prevent / HIV proviral DNA.

prevent / CCR5 gene / manage or cure / HIV proviral DNA.