Questions From the Hat

What cells in a patient will be damaged by chemotherapy?

-DNA damage so profound cancer cells can not survive -All dividing cells could be targeted -bone marrow, hair follicles

4. What are two reasons why rapidly dividing cells such as cancer cells need more glucose to survive as compared to quiescent cells?

1. cancer cells need sugar to divide and proliferate while quiescent cells are dormant 2. cancer cells underutilize mitochondria 1. cancer cells need sugar to divide and proliferate while quiescent cells are dormant 2. cancer cells underutilize mitochondria 3. Over utilize glycolysis Cancer cells exhibit warburg effect

The dissociation constant for biotin-streptavidin interaction is around 10^-14 molar. If you had a ~10 femtomolar solution of each biotin and streptavidin mixed together, about what fraction of the biotin would be bound to streptavidin?

10^-14 /10^-14=1

12. What are the two chemical moieties that conjugate in click chemistry, and which one is more commonly found in biological systems?

Azide and alkyne In contrast to ketone and aldehyde, there are hardly any azides occurring in biological systems. Azides possess highly intrinsic energy but no natural reaction partner (King and Wagner, 2014), have small sizes and neutral overall charge, and finally they are kinetically stable under physiological conditions

What is the Warburg effect?

Cancer grabs so much glucose because from one glucose molecule you only make 4 ATP through glycolysis underutilize their mitochondria cancer cells have hyperactive PDK so pyruvate is changed to lactate and shunted away from ox phos

3. How might cancer cells evolve to be resistant to the radiosensitizing strategy discussed in lecture?

Cells with less receptors will develop resistance because they won't be targeted as much by doxorubicin Cancers upregulate NSTRI, dox nanoparticle binds to and releases Cells with less receptors will develop resistance because they won't be targeted as much by doxorubicin Cancers upregulate NSTRI, dox nanoparticle binds to and releases doxorubicin

What evolutionary or developmental benefit is there for CDKIs to aid in assembly as well as inactivation of CDKs?

Functional CDKI has to be present for CDK-cyclin complex to form in the first place (analogy, a gun needs a properly working safety to operate). The inhibitor can also act to inhibit the CDK-cyclin complex action to slow the progression of the cell cycle.

What cell cycle phase transitions are typically checked and sometimes blocked and why?

G1→ S: checks for DNA damage, if there is damage p53 will be activated, DNA damage G2→ M: cell division, checking for DNA damage Don't want errors to be replicated in new cells G1: checking to make sure cell can support DNA replication, checking if cell has necessary proteins for S phase S phase: checking and will halt if DNA is defective, checking if DNA has replicated properly G2: will prevent cell from going into mitosis if DNA damage is detected. M: will check that sister chromatids are attached to microtubules

You are marooned on a desert island, and out of boredom you decide to do some molecular biology. You have garbage washed up on the sand, including glass bottles and halogenated plastic. Which could be better used to adsorb DNA and which protein?

Halogenated plastic: DNA Proteins: tend to passively absorb to hydrophobic surfaces→ glass because glass is hydrophobic More protein absorbed on glass than plastic DNA does not bind silica or glass DNA tends to bind to plastic surfaces Halogenated plastic is polar and so is DNA

11. If you wanted to turn on the expression of a gene, would you use CRISPR-i, CRISPR-a, or plain CRISPR?

In CRISPRa system, dCas9 is fused or interacts with transcriptional activators leading to gene expression upregulation CRISPR-i leads to gene expression repression

13. Name a ligand and receptor for one cell signaling pathway. Is this pathway involved in cancer progression?

Notch Ligand and Notch receptor Notch acts as a tumor suppressor Notch ligand & Notch receptor Yes, it is involved in cancer progression Upregulation of notch transduction pathway leads to upregulation of multiple other pathways leading to... - Anti-Apoptosis - Cell Cycle Progression - Cell Proliferation/Differentiation Over upregulation of notch receptors is oncogenic

What would be two problems you might have trying to probe a Western blot with two primary antibodies at the same time on the same blot, even if the antibodies are of different species? What is a way around this?

Probing separately prevents non specific binding and background noise, Way around this is to cut up paper This will reduce amt of antibody we need because less surface area

Which type of cells would be more likely to pick up mutations that lead to cancer, progenitor cells or stem cells, and why?

Progenitor cells have a short life span (error prone DNA repair, less healthy mitochondria → can turn into cancer) Progenitor is answer Stem cells self renew and go on to produce progenitor cells Tissue cell have long lifespan

What is the difference between plasma and serum, which is typically added to cell culture and why?

Serum is source of growth and adhesion factors, hormones, lipids, and minerals for the culture of cells in basal media. Serum is the liquid that remains after the blood has clotted. Plasma is the liquid that remains when clotting is prevented with the addition of an anticoagulant. Want to use serum in cell culture because it has protease inhibitors that can neutralize the protease in trypsin..

What is the defining property of stem cells?

Stem cells self renew and go on to produce progenitor cells Stem cells have better DNA repair systems so they are less likely to be oncogenically transformed One stays stem cell, the other is progenitor after cell division

What is telomerase and reverse transcriptase?

Telomerase is the enzyme expressed in stem cells, extends the ends of the chromosomes. Telomerase is expressed only in stem cells, progenitor does not have telomerase Reverse transcriptase is an enzyme that makes complementary DNA from RNA template

Define apoptosis and name a protein that protects cells from apoptosis.

apoptosis is programmed cell death. this usually happens when Bax and Bak oliogomerize and form a pore to release cytochrome C into the cytoplasm BCL-2 doesnt allow for oliogmerization and is anti-apoptotic (BCL-2, MCL 1, BCL-x)

Name one proto-oncogene and one tumor suppressor gene

proto-oncogene: HER2 tumor-supressor: p53,p21,p16

15. Why are bacterial epitopes needed during immunization to promote adaptive immunity?

used to teach the body that certain foreign cells are harmful since the innate system will be able to recognize the epitopes as harmful. use epitope in parallel with antigen to teach body T and B cells can recognize bacterial epitope

14. What two general genetic approaches would you use to prove definitively that a specific gene had a specific function?

you could knockout a gene and see if the function is no longer there (CRISPRi cas9) CRISPRa guides in promoter and gene in a cell that normally does not exhibit the function Use CRISPR-a to turn on the gene in question in a cell where this gene is not normally expressed. See if the the cells starts showing the suspected function.