Biotech Test Practice

What is our epigenome, and how does it relate to protein synthesis and gene expression?

It is the pattern of gene expression in our cells. This relates to protein synthesis because this determines the amount of each protein that is made. This relates to gene expression because, based on our epigenome, some genes will be expressed, overexpressed, underexpressed, stopped, etc.

What is the difference between our genome and our epigenome?

Our genome is the actual DNA, the ATCGs. Our epigenome is how those ATCGs are expressed to make proteins.

How do methyl groups (methylation of our genes) affect gene expression, and where do they attach?

It turns genes off. They attach to cytosine.

If the methyl groups bind upstream of the gene at the promoter region, how does it affect transcription factors and gene expression?

If a methyl group were to attach to the promoter, it would silence the gene, thereby allowing for the sequence to not be transcribed and for gene expression to diminish or die.

How do acetyl groups affect gene expression, and where do they attach?

They help with increasing gene expression. They attach to the histones and loosen the DNA from them, allowing for genes to be turned on.

What is epigenetic therapy and how does it work?

It is a therapy, often used for cancer patients, to help alter your epigenome rather than changing your DNA sequence. It works by helping to activate certain genes that may be helpful or deactivate genes that may be harmful.

Our genome is , but our epigenome is _.

Fixed, changeable

Why are different types of cells in your body different when they all have the same DNA sequences and genes?

Because in each type of cell, they are expressing different genes, therefore differentiating them

What are histones, and how do they relate to epigenetics?

They are what our DNA wraps around, and based on how loose or tight they are wrapped, different genes are turned on or off.

Compare and contrast methylation and acetylation

Methylation: uses methyl groups to attach to the DNA itself and block transcription tools from binding to the DNA.

Acetylation: uses acetyl groups to attach to histones and loosen the DNA from the histone, allowing for a gene to become active

As methylation increases, production of mRNA _.

Decreases

As acetylation increases, production of mRNA .

Increases

Can epigenetic patterns be inherited?

It is possible, however, it is very rare. Most of the time, our epigenome resets in our offspring

What environmental factors affect our epigenome?

Diet, exercise, toxins, stress, hormones, maternal care, etc.

How does our epigenome affect our behavior, and how does our behavior affect our epigenome?

Based on our epigenome, with some genes expressed while others not, it can change what proteins are produced and therefore what cells do. Based on our behavior, such as diet, we can alter our epigenome.

​​What are the characteristics that all stem cells possess that make them special?

They're capable of dividing and renewing themselves for long periods, they're unspecialized, and they can give rise to new specialized cell types

What does undifferentiated mean regarding cells?

They are a cell not yet assigned a specific purpose

Pluripotent

The cell can transform into any cell type (except placenta). These are commonly embryonic stem cells

Multipotent

The cell can transform, but only into a limited number of cell types. These are commonly adult stem cells

Adult Stem Cells

Found in specialized cells in a tissue or organ, such as fetal tissue, cord blood, and adult cells. They are multipotent, so they can form several different cell types. Advantages: They match the parent's cells, there's less controversy, and there's more research on these cells. Disadvantages: they exist in small numbers, so it's difficult to get enough for therapeutic work, they're more difficult to identify, isolate, purify, and grow in the lab, and cell replacement therapies require unlimited quantities of donor cells, which adult stem cells often can't provide. We have a very high understanding of these

Embryonic Stem Cells

Found in 5

iPS (Induced pluripotent stem)

Created by reverting adult stem cells. They are pluripotent, so they can form any cell type. Advantages: does not involve creation or destruction of an embryo, cells can form any cell type, and less tissue rejection potentially because it's from the patient's body. Disadvantages: Less research into it, epigenetic patterns questions, potential for rejection, and questions regarding cell behavior throughout their lifespan

What is a blastocyst, and with what type of stem cell researcher is it associated?

An early

Why is embryonic stem cell research controversial?

Removing the embryonic stem cells destroys the embryo, they're destroying life, and science is going to far

What are the myths with regards to embryonic stem cell research?

Researchers are removing a mother's embryo, the embryos have recognizable body parts, and it's illegal

What are the facts with regard to embryonic stem cell research?

The blastocysts were created in a lab, not a woman's body, there are no recognizable body parts on the embryo because the cells haven't differentiated, and there are no laws against research into it

What is the main purpose of a scientific journal article?

To professionally share your research to benefit the rest of the scientific community

What is the formatting for how you wrote the journal article?

Double

What are the main sections found in a journal article (in order)?

Title page, Abstract, Introduction, Methods, Results, Discussion, Acknowledgements, References

What is the purpose of the Title in a journal article, and what must be included in the title?

To show the title of your paper, who wrote it, and where the research was performed. Title of article, Author, Lab Name, and Lab Address

How is the header different from the title in a journal article?

The header should be a shortened version of your title

What is the address in a journal article, and what is its purpose?

Where the research was performed, allowing the lab to receive credit for the research

What is the importance of the order of the authors in a journal article?

The first author is your lead author

What content is included in the abstract of a journal article?

A quick summary of your paper, including some details from every section except acknowledgements and references

What information is included in the introduction of a journal article, and what is its purpose?

Your research question, your justification behind your research, background on subjects needed in order to understand what's happening in the lab, and an overview of your methods. Its purpose is to introduce the background behind your subject and your intended research into the subject

What is the purpose of the results in a journal article?

To state the results of your research

True or False: You can draw conclusions about your results in the Results section

False

With every figure, graph, picture, or table in a journal article, what is included?

A caption in 8 pt font.

How do you write captions for images/graphs/tables in journal articles?

You must put picture/graph/table and a number, describe what's happening in the picture/graph/table in detail, and reference that picture in your text

In what sections of a journal article are the results interpreted?

The discussion

Who is typically acknowledged in the acknowledgement section of a journal article?

Donors, lab peers, and peer editors

Where do you find in

text citations in a journal article?

What is the general format for a reference in the references section of a journal article?

Authors (Date of Publication). Title of article. Title of Online Periodical, volume number (issue number), page number range. DOI.

What is the general format for an in

text citation in a journal article?

How do you correctly write a scientific name?

Genus (capitalized) species

What are some words/types of words you never should use in a Journal Article?

This proves…, Present tense

What types of things can model organisms be used to study?

Genetics, developmental biology, human disease, and things that are unfeasible or unethical in humans

What are examples of commonly used model organisms (One plant, invertebrate, vertebrate, prokaryote, and single

celled eukaryote)?

What are the main characteristics of a good model organism?

Traits/genetics in common with humans, small, easy to house/breed, reproduce quickly with short life cycles, reproduce in large numbers, inexpensive

What model organisms did we work with this year in class?

Planaria, E. coli, fruit flies

What are the key characteristics of Planaria that make them ideal model organisms for regeneration?

Planaria can regrow body parts, they require very little food, they are small, etc.

What are the key characteristics of Fruit flies, as to why we use them in our lab?

Fruit flies reproduce quickly, have short life cycles, and share a lot of genetic information with humans

What is the procedure for anesthetizing fruit flies?

Transfer them into a gas chamber in a fume hood using a funnel, take a wand with FlyNap in it and stick it into the gas chamber with the stopper still on, then once they aren't moving very much, transfer them into a petri plate

What are the key features to identify a male versus a female fruit fly?

Sex combs (males), size (males are smaller), black butt (males), stripped butt (females)

What does genetically modified mean?

It means that you are using technology to change the DNA of an organism, like a plant or animal

What is a transgenic organism?

An organism that has a gene from another species inserted into its genome

What technologies are used to create genetically modified organisms?

Recombinant DNA technology (inserting DNA into a cell), Target Mutation technologies (ZFN, TALENS), and CRSPR

What is a recombinant DNA molecule, and what enzymes are required to make one?

DNA created in a lab by combining DNA from different species. Restriction enzymes and DNA ligase

What are examples of ways that creating transgenic organisms can be useful to society?

Improve the economy, improve food security, improve human health, treat diseases, etc.

What is a cloning vector, what are some examples, and what role do they play in creating transgenic organisms?

The thing you attach to DNA so it can be inserted into a cell. Plasmids, stem cells, viruses, and bacterial artificial chromosomes. These help to transport the DNA

How does recombinant DNA technology compare to CRISPR?

Recombinant just inserts the DNA, while CRISPR edits the DNA

What is gene therapy?

Editing the genes of someone to prevent or cure a disease

What size bands did we use to identify that a plant was genetically modified in the GMO lab?

A band between 150 and 180 bp and a band for the 35s promoter (125 bp) to signify genetic modification

Why did we do the GMO lab?

To test common foods and plants for if they are genetically modified and to refresh our skills in doing gel electrophoresis and using equipment

What are the applications of CRISPR?

Gene insertion (insert a gene into the DNA), Gene Correction (Delete base pairs that cause mutations), Gene Activation (Put in transcriptional factors to areas to activate desired genes), and Gene Kockdown (Put in stop codons)

What can you do with CRISPR that cannot be done with other technologies?

Inserting new genes into the DNA and activating other genes

What are concerns related to CRISPR research?

It could go on to be used to edit embryos and the human germline to make people as best as possible genetically, which would then have the changes spread through generations

How does CRISPR work?

Cas9 and Guide RNA or gRNA are inserted into a cell. They both then head to the DNA in the nucleus. The gRNA's job is to guide Cas9, our enzyme, to the DNA and tell it where in the DNA to cut. The cell then activates one of two repair methods to fix the DNA: Non

In the Out of the Blue CRISPR lab, what was the overall purpose of the lab, what was included in the repair template, and why did we use blue/white light as an indicator of success?

To learn how to CRISPR edit a gene in bacteria so it wouldn't turn blue. The LacZ gene, when in use, creates an enzyme to digest lactose and blue pigment. Our goal was to turn this gene off using CRISPR. The repair template contained a stop codon. We used blue/white light as an indicator because it's able to be easily observed without the need for DNA sequencing.

Why did we heat shock in the Out of the Blue CRISPR lab?

So the Cas9, the Donor DNA, and in one plate the Guide RNA could make their way into the bacterial cells.

Why did we keep the samples at room temperature after heat shock in the Out of the Blue CRISPR lab?

We kept it at room temperature so it could continue to grow and repair.

Why did we add room temperature LB broth to the bacteria in the Out of the Blue CRISPR lab?

We added LB broth to feed thm and give materials for them to repair so they wouldn't die.

How did you know visually you were successful in completing the Out of the Blue CRSPR lab?

We knew if we were successful visually if the colonies were white.

Why did you use HDR (and not NHEJ) in the Out of the Blue CRISPR lab?

So that we could insert a new DNA sequence of our choice

What was the significance of the 2 different types of plasmids in the Out of the Blue CRISPR lab?

One had the Donor DNA and one had the Donor DNA + Guide RNA, and this is what carried the new sequence to edit the gene

What was also on the plates for the bacteria to grow in the Out of the Blue CRISPR lab?

LB broth, kanamycin and spectinomycin

Did you need to be concerned about sterility and working in the BSC in the Out of the Blue CRISPR lab?

No, we didn't because this strain of E. coli is not known to cause harm in humans, the kanamycin kills any other bacteria that may grow, and the spectinomycin kills any other bacterial Donor DNA.

What does it mean to make a cell competent and how did we do this in the Out of the Blue CRISPR lab?

We did this by heat shocking them. This means that the membrane around the cell will have holes in it where the gRNA and the Donor DNA can go through the phospholipid bilayer so the bacteria takes up the gRNA and the Donor DNA

What other method could use besides color of the bacteria to confirm successful gene editing in the Out of the Blue CRISPR lab?

DNA sequencing

What is a gene?

A sequence in DNA that codes for a protein

What does it mean to silence a gene?

To silence a gene would mean to make it so the protein made from that gene isn't being made as much or not at all

What does gene silencing have to do with protein synthesis/gene expression?

Gene silencing determines how much of that protein is made using protein synthesis and how much that gene is thereby expressed

At what stage/step of protein synthesis does the RNAi system impact?

Translation

What does RNAi stand for?

RNA Interference

What is the RNAi system?

It is a system designed to detect RNA of viruses attempting to invade the cell and destroy all copies of it and ones that look similar to it

How could the use of the RNAi system help us treat disease?

We can insert double

How could RNAi help us understand the function of different genes?

It helps us determine the function because now we get to see what the outcome would be without a certain gene, and thereby identify the purpose of a gene because of its absence

What types of diseases could be helped through RNAi therapy?

Viral infections, cancer, cardiovascular disease, metabolic disorders, neurologic diseases, etc.

What types of diseases could NOT be helped through RNAi therapy?

Diseases where the gene is not functioning at all.

How could Planaria be used to study RNAi?

We could use them to study RNAi by giving them double

How did scientists first discover RNAi?

They were genetically engineering petunias to make them more purple, but instead of more purple, they became white

Why is RNAi therapy not a permanent cure for a disease?

Because it only destroys RNA copies of that gene in one cell, not all of them

What do scientists think the natural purpose of RNAi in a cell is?

To get rid of doublestranded RNA from viruses attempting to invade the cell

What are the challenges of using the RNAi system for therapeutic purposes?

Delivering the doublestranded RNA to the right cells, the unknown effects of genes, and the long

How are we using RNAi in fruit flies in the Fruit Fly lab?

We are crossing females with the Gal4 driver with males with UAS, RFP, or NITO and RNAi, which will trigger the RNAi system to get rid of all RNA associated with lipid accumulation

How will we test if we were successful in turning off the lipid accumulation gene in the Fruit Fly lab?

We will put them in water and see if they sink or float

What is the significance of virgin week in the Fruit Fly lab?

This is the week we are releasing the fruit flies 8 hours before class to guarantee they didn't store the male sperm and are virgins, and we are then collecting all the females to create offspring with the males that have the UAS, RFP, or NITO and RNAi so we can see if the RNAi gets rid of the lipid accumulation gene.

PCR Technology

Used to create thousands of more copies of DNA for further experimentation. Based of DNA replication. In this, we take the DNA, break it apart, give it the tools to create it's other half, and then it repairs itself by creating the opposite missing side, thereby giving us more DNA

DNA Profiling

Each person has a polymorphic region in their genome unique to them, and we can use that area to identify someone.