Micro

Which of the following describes how E. coli was transformed in the experiment described in Exercise 10-3?

the E. coli cells were chemically competent and heat shock was used to get DNA into the cells

If you wanted a bacterial cell to make a protein from a human gene, how would you amplify the human gene? {hint: look up RNA processing in Eukaryotic cells}

use reverse transcriptase to make a cDNA of mRNA from gene of interest then use PCR to amplify the cDNA

Which of the following is function of viral capsid? Select ALL that apply.

virion shape attachment to host cell protection of nucleic acid

Part 6: Look at the image of pUC19 below. You decide to insert the charming gene PCR product that has been digest with XbaI and SmaI into the pUC19 vector that has also been digested with XbaI and SmaI. How will you "glue" the digested PCR product into the digested plasmid?

with ligase

how was the patient's sickle cell anemia treated with CRISPR?

CRIPSR was used to increase the production of fetal hemoglobin

Each infected cell can release [a] copies of virus before the cell finally breaks down and [b].

Each infected cell can release millions copies of virus before the cell finally breaks down and dies.

When entering the lysogenic cycle, bacteriophage replication stops after which of the following steps?

Entry

In the presence of arabinose, RNA polymerase [a] bind to the promoter and transcription is turned [b]

In the presence of arabinose, RNA polymerase can bind to the promoter and transcription is turned on

If a scientist wants to use CRISPR-Cas system to delete a gene that contains the following sequence ATGCCA, which of the following would be the correct guide RNA for the CRISPR-Cas system?

UACGGU

How can we ensure we are only amplifying and detecting SARS-CoV-2 viral sequence?

Use primers that are specific to SARS-CoV-2 nucleic acid

Which of the following terms refers specifically to the extracellular state of a virus?

Virion

All of the following are general characteristics of viruses EXCEPT:

Visible by light microscopy

When bacteriophage's DNA is inserted into a bacterial cell's chromosome, it is called a [c] which [d] excise from bacterial cell chromosome and enter the lytic cycle.

When bacteriophage's DNA is inserted into a bacterial cell's chromosome, it is called a prophage which can excise from bacterial cell chromosome and enter the lytic cycle.

Where was CRISPR discovered?

bacterial cells

RNA viruses that do not produce reverse transcriptase are unable to undergo provirus formation. Why?

because without reverse trancriptase, the virus cannot make the DNA that will insert into the host's chromosome

Part 9: Look back at the image of pUC19 above. This plasmid has a lacZ gene as a reporter gene. The charming gene is inserted into the plasmid at the XbaI and SmaI sites. How would you screen for colonies that have the recombinant plasmid (plasmid containing the charming gene)? {Hint: Look at Figure 12.5 in your book}.

colonies with recombinant plasmids will be white when grown on agar plates containing X-gal

Look at the image of the viruses below. What is the best description of their overall shape?

complex

The animal virus, Tarzan, infects muscle cells in its human host. This virus has a +ssRNA genome. In order to be replicated, this virus needs more copies of its genome and it needs to have its viral proteins made as well. Can the host cell's translation machinery make viral polypeptides directly using the information on the Tarzan +ssRNA genome?

yes

Part 8: You transform B. beasti cells with the recombinant pUC19 plasmid containing charming gene in its MCS. How would you select colonies that have the plasmid?

grow cells on media containing ampicillin, bacteria that grow in presence of ampicillin have the plasmid

Look at the figure of a qPCR report for SARS-CoV-2 below. Which of the following would be a negative control.

host cell DNA

Interpret the SARS-CoV-2 qPCR report below. What is the result for Patient #3?

inconclusive

What type of lab is Quest labs?

independent reference laboratory

Interpret the SARS-CoV-2 qPCR report below. What is the result for Patient #2?

positive

transgenic organisms

organisms that contain functional recombinant DNA

Prions are [a] and [b] be inactivated by an autoclave.

Prions are proteins and cannot be inactivated by an autoclave.

Prions are infectious because they are associated with which of the following phenomena?

Protein folding

Recall the central dogma of molecular biology. Where does reverse transcription fit in with the central dogma? Match each keyword with the number in Figure 4 below:

Question Selected Match 1 A. DNA 2 B. transcription 3 C. RNA 4 D. translation 5 E. protein 6 F. reverse transcription 7 G. cDNA

RNA polymerase from cells makes ____ using ____ as a template.

RNA; DNA

What enzyme is used to make a cDNA copy of viral RNA?

Reverse transcriptase

Look at the figure of a qPCR report for SARS-CoV-2 below. Which of the following would be a positive control.

SARS-CoV-2 RNA

a] is the virus that causes COVID-19. The virus uses its [b] to attach to [c] on the surface of cells. Once inside the cell, the virus releases its [d] genome.

SARS-CoV-2 is the virus that causes COVID-19. The virus uses its spike to attach to ACE2 on the surface of cells. Once inside the cell, the virus releases its RNA genome.

Assume that the qPCR is set up and ran correctly, what else could contribute to ambiguous results for a SARS-CoV-2 test from a patient sample?

The PCR can be ran correctly but a patient could be asymptomatic and have a slight increase in anti-SARS-CoV-2 antibodies, the antibodies can make the results inconclusive.

Each plaque represents how many phage particles?

1

Put the descriptions of what happens in PCR in order.

1. DNA strands unwind 2. Oligonucleotides (primers) base-pair with complementary DNA sequence 3. DNA polymerase makes complementary strand of DNA by adding nucleotides to 3' end of oligonucleotides

If you have one DNA molecule at the beginning of PCR, how many would you have after 5 cycles of PCR?

32

How many plaques are in the blue box on the plaque assay plate below? ____

4

Match the labeled part of the multiplication curve for a bacteriophage with its best description.

A B. when virus binds to cells B A. when virion enters cells C C. when virions are released from cell D D. number of virions released per bacterium

Match the stage of the lytic replication cycle in the diagram below with its best description.

A E. Phage attaches to surface of host cell B C. Phage DNA enters host cell C D. phage DNA replicates and phage proteins are made D B. new phage particles are put together E A. bacterial cell lyses, releasing newly made phages

Look at the plate below and select the correct labeling of A and B.

A is bacterial cells, B is plaque

Which of the following is the best definition for CRISPR-Cas9

A system that uses small guide RNAs to bind target DNA and guide the sequence-specific cutting of target DNA

multiple cloning site (MCS) lacZ a gene that allows someone to distinguish between cells that have a plasmid containing gene of interest inserted and cells that have a plasmid without gene of interest inserted amp

B. contains many restriction enzyme recognition sites that are used for inserting DNA into the plasmid C. reporter gene A. antiboitic resistance marker that allows one to determine if bacteria have the plasmid or not C. reporter gene

Prince Charming is interested in isolating phage from the moat that surrounds the castle. He gathers 100 ml of moat water and filters it though a 0.45 micron membrane filter. Which of the following correctly states what will likely be trapped in the filter and what will likely be in the filtrate (the liquid that passed through the filter)?

Bacteria will be in filter and phages will be in filtrate

Part 7: Now that we have inserted the charming gene into pUC19, we have to get the recominant plasmid into Beastae beasti. Not all bacteria are naturally competent. Watch the video below about two methods to "help" bacteria take up DNA and then select the true statement below.

Bacteria, like E. coli, can be made to take up DNA after being shocked with electricity or being treated with calcium ions and heat.

A virus that infects bacteria is called a(n)

Bacteriophage

Which of the following are sources of nucleic acids that you would expect to find in a patient sample? Select ALL that apply.

DNA from human cells in nasal cavity RNA from human cells in nasal cavity RNA from viruses in nasal cavity DNA from bacterial cells in nasal cavity

Which of the following structures could be found in/on a virion? Select ALL that apply.

DNA genome RNA genome capsid reverse transcriptase phospholipid bilayer

Which of the following structures could be found in/on both cells and virions? Select ALL that apply.

DNA genome RNA genome phospholipid bilayer

DNA has a [a] charge. In gel electrophoresis, DNA migrates towards the [b] electrode.

DNA has a negative charge. In gel electrophoresis, DNA migrates towards the positive electrode.

Which of the following about gel electrophoresis is correct?

DNA is separated in gel electrophoresis based on size

Recombinant DNA

DNA made of 2 or more pieces of DNA combined by humans into a sequence that doesn't exist in nature

Doctors use laboratory tests to help [a] disease, [b] treatment for a disease, evaluate patient [c] to a treatment, or to [d] the course of a disease over time.

Doctors use laboratory tests to help diagnose disease, plan treatment for a disease, evaluate patient response to a treatment, or to monitor the course of a disease over time.

It does not matter which bacterial species you grow a particular phage in because bacteriophages are not host-specific.

False

Taxonomic groupings of closely-related viral genera are called ____________________, and are given names ending with the suffix - viridae.

Families

Use the website Enzyme Finder from New England Biolabs to determine which enzyme below cuts DNA such that the DNA fragments have blunt ends.

FspI

Which of the following techniques have been used to grow virulent bacteriophage. Select ALL that apply.

Growing phage in fluid bacterial culture medium Growing phage in agar plate in presence of bacteria

If the transformation went as expected, which of the following would you see after plating E.coli from +DNA tube on LB/amp or LB/amp/ara plates.

Growth on both LB/amp and LB/amp/ara plates

HIV is a retrovirus with a +ssRNA genome. It uses [a] to make DNA copy of its genome that then gets inserted into a host cell's chromosome. Once its DNA is inserted into the host chromosome, the viral DNA is called a [b] and [c] host chromosome

HIV is a retrovirus with a +ssRNA genome. It uses reverse transcriptase to make DNA copy of its genome that then gets inserted into a host cell's chromosome. Once its DNA is inserted into the host chromosome, the viral DNA is called a provirus and can excise from host chromosome

In qPCR of the viral cDNA generated in Figure 4 above, the [a] viral sequence in the sample the more [b] will be detected

In qPCR of the viral cDNA generated in Figure 4 above, the more viral sequence in the sample the more fluorescence will be detected

Read Part III from The Power of a Test.pdf case study. Then, look at positions under clinical laboratory at Laboratory Science Careers. If you chose a career in a clinical laboratory, which position would you choose and why?

If I chose a career in the clinical laboratory field I would either chose Humanitarian and work on Medical Mission or Forensics and do Crime Scene Investigations. Both of these field are of great interest to me. I lean towards them because I have worked in the Criminal Justice Field for over twenty years and I have a passion for upholding the law and solve complex problems. However, I also had a dream to become a Nurse when I was younger because I have a passion for wanting to help people and make them better. I always those about going on a Medical Mission in order to help provide basic healthcare to those that cannot afford it or those that do not have access to modern medicine. I would love to give back and feel like I had a hand in eradicating disease. The investigative side of me would love to help solve crime and to help hold those that committed the crime accountable for their actions.

n a plaque assay, phage and bacteria are grown on agar medium, after a period of incubation, phage [a] the bacterial cells resulting in [b] on the plate known as plaques.

In a plaque assay, phage and bacteria are grown on agar medium, after a period of incubation, phage lyse the bacterial cells resulting in clearing on the plate known as plaques.

In both traditional and quantitative PCR DNA is [a], but in quantitative PCR, [b] probes are used to measure the amount of DNA.

In both traditional and quantitative PCR DNA is amplified, but in quantitative PCR, fluorescent probes are used to measure the amount of DNA.

Let's say that the sequence of the +ssRNA genome from Tarzan virus is 5'AUGCCA 3', the sequence of the complementary strand would be [a] which [b] an exact copy (or clone) of the Tarzan +ssRNA genome; therefore, the viral enzyme, [c] would use this complementary strand as a template to make more [d].

Let's say that the sequence of the +ssRNA genome from Tarzan virus is 5'AUGCCA 3', the sequence of the complementary strand would be 3'-UACGGU-5' which is not an exact copy (or clone) of the Tarzan +ssRNA genome; therefore, the viral enzyme, RNA-dependent RNA polymerase would use this complementary strand as a template to make more viral genome.

In the absence of arabinose, RNA polymerase [a] bind to the promoter and transcription is turned [b]

Look at Figure 10.9. In the absence of arabinose, RNA polymerase cannot bind to the promoter and transcription is turned off

All of the following could potentially be utilized as vectors EXCEPT:

Primers

When we think of viruses, especially in our current pandemic, we tend to only see them as the obligate parasites they are, but there are ways in which we can use viruses to improve our lives. Find a secondary source (news article) about a "good" use for viruses. Complete the following activities: 1. Provide the citation for the article using the following format: Lastname, F. M. (Year, Month Date). Title of article. Title of Publication. URL 2. Summarize the article in 3-5 complete sentences. 3. Suggest another use for viruses based on what you learned in your article.

Newman, T. (2020, January 6) How 'good' viruses may influence health. Medical News Today. https://www.medicalnewstoday.com/articles/327167 This article discussed the good viruses found in the body. The author talked about how we have many viruses in our bodies that do not cause disease. He stated that scientist have just recently started looking at these viruses and how they are beneficial to us. He said the main focus of study has been the viruses in the gut. He explained that some of these viruses go after bacteria. These bacteriophages code the bacteria and attack and eliminate specifics cells and how the study of phage therapy is on the rise. He stated that antibiotics kill all bacteria even the good kind and phage therapy can start just those that make human ill. Another use for viruses would to help eliminate disease that is currently not curable and fixing mutation in certain DNA codes.

Animal viruses can be cultured in the laboratory using all of the following EXCEPT:

Nutrient agar plates

[a] is a process used to make copies of DNA in the lab. The two strands of DNA are held together by [b] bonds which are broken in this process by [c].

PCR is a process used to make copies of DNA in the lab. The two strands of DNA are held together by hydrogen bonds which are broken in this process by heat.

A [a] is a DNA molecule used to carry a gene of interest from one organism to another. An example of this is a [b] which is an extrachromosomal, circular piece of DNA.

Part 3: The PCR worked! Now we have to get the charming gene into B. beasti. First, we have to learn how to get a gene of interest form one organism to another. A vector is a DNA molecule used to carry a gene of interest from one organism to another. An example of this is a plasmid which is an extrachromosomal, circular piece of DNA.

he SARS-CoV-2 genome is less than [a] nucleotides long. [b] makes more viral genome and the infected cell uses its translation machinery to make more viral [c]. Next, new viruses are [d] and then [e] from the infected cell.

The SARS-CoV-2 genome is less than 30,000 nucleotides long. RNA makes more viral genome and the infected cell uses its translation machinery to make more viral protein. Next, new viruses are assembled and then released from the infected cell.

Biotechnology

The use of technology to control biological processes as a means to meet societal goals.

Why do viruses have to infect host cells?

They are dependent on the host cell's structures and enzymes for their replication.

DNA fragments are loaded into a gel and a current is applied. After an hour, a picture of the gel is taken. Below is a diagram of the gel. Which DNA fragment is the largest?

a

Genetic engineering

a form of biotechnology in which genetic information is changed to make a new product.

The DNA binding protein, araC, is best described as

a transcription factor

Which of the following are types of samples that might be collected from patients to use for laboratory testing?

all of the above urine saliva sputum blood all of the above

Part 10: Let's think a little more critically about the experiment. After transfroming the bacteria with the ligated plasmid mixture, you plate the mixture on the following plates: agar only agar with ampicillin agar with ampicillin and X-gal

all of the blue colonies on plate 3 contain bacteria with pUC19

In its role in regulation of arabinose operon, arabinose is best described as

an inducer

Read about proto-oncogenes, oncogenes, and tumor-suppressor genes here. Then choose the correct statement below.

an oncogene causes a cell to become cancerous

If araC were mutated such that it cannot bind to arabinose, what would be the result?

arabinose operon would be "off" in presence or absence of arabinose

Gene therapy of which type of cell would result in the traits being passed on to offspring?

germline

Host specificity of a virus is due to

interactions between viral and cellular surface molecules

Why is lysogeny helpful to a virus?

it's genetic material can be easily passed onto future generations of host cells

During __________, an animal virus remains dormant inside the cell.

latency

In which viral life cycle are bacteriophages made immediately?

lytic cycle

Which of the following leads to the destruction of the host cells?

lytic cycle

The envelope of a virus is derived from the host's

membrane structures

What samples are typically collected from patients suspected of coronavirus exposure?

nasopharyngeal swabs

Interpret the SARS-CoV-2 qPCR report below. What is the result for Patient #1?

negative

Can RNA polymerase from a host celll use the +ssRNA genome from Tarzan virus as a template to make complementary RNA strands?

no

In the above video, scientists introduced DNA into a somatic cell. Would this DNA be passed on to offspring?

no

Which of the following do ALL viruses/virions have? Select ALL that apply

nucleic acid genome envelopes spikes capsid

How are more HIV particles made after provirus formation? Reminder: HIV is a +ssRNA retrovirus.

provirus excises from chromosome and reverse transcriptase makes more HIV genome and host cell's translation machinery makes more HIV protein

Which of the following statements about restriction enzymes is true?

restriction enzymes cut DNA at specific sequences

Which of the following structures could be found only in cells but not virions? Select ALL that apply.

ribosome RNA-dependent RNA polymerase glycolytic enzymes

Why is a thermostable DNA polymerase required for PCR?

so that a scientist doesn't have to add more DNA polymerase after the denaturation step in EVERY cycle of PCR

How does HPV cause cancer?

some strains carry oncogenes

The component(s) of a virus that is/are extended from the envelope for attachment is/are the:

spikes