Molecules Exam 1b

Question 1

Protein targets: GPCRs

Answer 1

They control the opening of ion channels by stimulation or inhibition of effector enzymes

Question 2

The first and second messenger of GPCRs

Answer 2

First: Ligand
Second: Effector enzyme

Question 3

What does the second messenger of GCPRs do?

Answer 3

Activate protein kinases for protein phosphorylation

Question 4

Explain how different diseases can help us understand the processes of each of them

Answer 4

Cancer is the product of an abnormal cell surviving and replicating. In a patient with Alzheimer’s, these abnormal cell processes always fail. Therefore, patients with Alzheimer’s have an extremely low chance of getting cancer. Could a treatment for Alzheimer’s be located in the mechanisms of cancer?

Question 5

Protein target: Enzyme-linked

Answer 5

Receptor on the cell surface bind with enzymes(ligands). This causes dimerization of the receptor. Dimerization causes phosphorylation of the target proteins which helps elicit a cellular response.

Question 6

What are the dominant forces in drug-target binding?

Answer 6

Noncovalent

Question 7

What is the target in enzyme-linked receptors?

Answer 7

Growth factors like insulin

Question 8

Protein target: Nuclear (intracellular) receptors

Answer 8

The ligands bind intracellular and transcription factors are ligand-activated. Has a slow effect.

Question 9

Target of nuclear receptors

Answer 9

Sex hormones and other steroids

Question 10

Protein target: Ion channels

Answer 10

Proteins that control the opening and closing of ion channels and, thus, the ions that pass through them.

Question 11

Which protein target is important for neuronal and cardiovascular function?

Answer 11

Ion channels

Question 12

Proteins that transport molecules across cell membranes

Answer 12

Transporters

Question 13

Biologic targets: Nucleic acids

Answer 13

These drugs usually work to inhibit or block replication, transcription, and/or translation by modifying nucleic acids (cancer drugs)

Question 14

Biologic targets: RNAi

Answer 14

Can target nucleic acids by binding to the complementary strand of RNA to stop replication. Double stranded RNA stops protein formation

Question 15

Biologic targets: Lipids

Answer 15

Drugs that bind to the cell membrane and change the permeability. This controls what can and cannot pass through the membrane

Question 16

Established target

Answer 16

The research has already been done on this target. Basically trying to make a drug that works on this target better than whatever is currently on the market by working better or having less side effects

Question 17

Novel target

Answer 17

No research has been done on the target. The proposed targets must be validated. Is way more harder to develop a drug this way

Question 18

Genotype effects on a drug response

Answer 18

Pharmacogenomics

Question 19

What is the purpose and role of target validation?

Answer 19

When the target, after being modified pharmacologically, is proven to be effective and safe for human disease in a long-term clinical setting

Question 20

Phenotype-based discovery

Answer 20

Find some compound first and then figure out how it works. You use initial drug screening to find a hit, and then optimize a target based on that. It is also unbiased

Question 21

Target-based discovery

Answer 21

Choose a target first, and then find some active compound that will work on the target. Hypothesis-based

Question 22

How does gene silencing help validate a target?

Answer 22

You knock out or knock down a gene in order to see if there is a change in function. If there is a change, then you know that that gene effects the disease.

Question 23

How does CCR5 work?

Answer 23

It is a receptor that helps replicate HIV. If you block it, then you stop the virus from replicating. If someone does not have this receptor, they will not get HIV even if they are exposed

Question 24

4 steps of target validation

Answer 24

1. Link gene to disease
2. Determine expression pattern in normal vs. disease tissues
3. Manipulate target
4. Find mechanisms of action via in vitro and in vivo assays

Question 25

How do antisense oligonucleotides work to silence genes?

Answer 25

They bind to complementary target mRNA in order to block the expression of any gene being studied. It kills the messenger. It is quick, rapid, and predictable

Question 26

How does RNAi work to silence genes?

Answer 26

A natural process to protect agains viruses and other elements that utilize dsRNA to self-replicate (their virus or disease)

Question 27

What are dsRNAs?

Answer 27

Double strand RNAs that lead to cell death and flu-like symptoms

Question 28

Negative control siRNA

Answer 28

An siRNA that has the same nucleotide composition but not homogenous to the genome (diverse)

Question 29

Positive control siRNA

Answer 29

All of the other reagents but NO siRNA

Question 30

When a gene from another species is inserted into its genome

Answer 30

Transgenic

Question 31

Gene replaced with non-functional mutant

Answer 31

Knock-in

Question 32

Constitutive gene knockout

Answer 32

Target gene is permanently disrupted

Question 33

Conditional gene knockout

Answer 33

Eliminated a specific gene in a certain tissue or time specific manner. Target is more precise, and the genes in the rest of the body are unaffected

Question 34

Reporter genes

Answer 34

Certain genes are chosen to be reporter genes because they affect the organism in a way that the characteristics expressed are easily identifiable and measured. They are indicators of whether the specific gene is taken up or expressed by the cell in the organism

Question 35

Cas9 role in CRISPR

Answer 35

Nuclease scissors cleave dsDNA which activates the double-strand break repair machinery (helps put it back together)

Question 36

CRISPR vs. RNAi

Answer 36

RNAi goes in and temporarily knocks down mRNA in the transcription stage. It also is naturally occurring. CRISPR is artificial and permanent

Question 37

What is the part of CRISPR that can act like an immune system if original gene comes back after editing?

Answer 37

TracrRNA/trRNA (trans-activating RNA)

Question 38

CRISPRi*

Answer 38

Targeted silencing of transcription and requires inactive Cas9 (dCas9) and sgRNA. These elements bind to DNA to halt transcription.

Question 39

Can bind to a receptor but produces less than max effect

Answer 39

Partial agonist

Question 40

Kd in relation to binding affinity

Answer 40

Koff/Kon, therefore a small Kd = a high binding affinity

Question 41

Indicator of potency

Answer 41

EC50

Question 42

The ability of a drug to produce a max response

Answer 42

Efficacy

Question 43

Tenacity with which a drug binds to its receptor

Answer 43

Affinity

Question 44

Competitive antagonist on a curve

Answer 44

Shifts curve to right; EC 50 changes, therefore potency changes. Emax remains the same

Question 45

Can competitive antagonists' inhibitory effects be overcome?

Answer 45

Yes, by adding a higher concentration of agonist (binds reversibly)

Question 46

Non-competitive antagonist on a curve

Answer 46

EC 50 remains the same, but the Emax is decreased.

Question 47

Can noncompetitive antagonists' inhibitory affects be overcome?

Answer 47

No, this is because they bind irreversibly. Primary effect of a noncompetitive antagonist is to reduce maximal effect

Question 48

Drug binds within the same site as the receptor's ligand

Answer 48

Orthosteric binding (most common)

Question 49

Bind to a site different from that of the orthosteric agonist binding site

Answer 49

Allosteric binding

Question 50

Explain the concept of Spare Receptors

Answer 50

Non-liner occupancy response coupling. Don't always have to occupy every receptor to get a max response. If there are 100 receptors available but only 10 are needed to reach max effect, the EC50 is 5

Question 51

TI equation

Answer 51

TI = TD50/ED50

Question 52

Drug is still binding but no effect is occurring

Answer 52

Desensitization

Question 53

RAPID decrease in drug response after a few doses of the drug. Increasing the dose CANNOT produce the same effect

Answer 53

Tachyphylaxis

Question 54

A gradual loss of response, person will acquire a resistance to the drug after prolonged use

Answer 54

Tolerance

Question 55

Down Regulation

Answer 55

Can lead to tolerance. Decrease in expression of a receptor in response to increased activation/drug. Meaning that even though you are taking more of the drug, the effect is decreasing (developing tolerance)

Question 56

Up Regulation

Answer 56

Increase in the number of receptors in the surface of the target cells, making them more sensitive

Question 57

Selectivity for different receptor subtypes

Answer 57

Receptor selectivity

Question 58

Selectivity for different signaling pathways coupled to the same receptor

Answer 58

Functional selectivity (biased agonism)

Question 59

Intrinsic toxicity (Type A)

Answer 59

Affects all individuals at the same dose, predictable, dose related

Question 60

Idiosyncratic toxicity (Type B)

Answer 60

Rare and unpredictable, unclear relation to dose, affects only susceptible individuals

Question 61

Basic assumptions made in safety testing

Answer 61

-Assume that animal toxicity will translate to that of humans -Animals are bred essentially pure, but humans are diverse -Even in a rigorous animal testing (1000-2000 animals testing) it is still nothing near millions of people -Dosage given to animals is highly regulated, but humans sometimes miss a dose or take too much

Question 62

Any effect that could lead to cell death

Answer 62

Cytotoxicity

Question 63

The inability of a drug to induce a mutation in a cell can be indicative of possible carcinogenic activity. Test the ability of a molecule to produce changes in DNA of a modified salmonella

Answer 63

Mutagenicity

Question 64

Hepatic Toxicity

Answer 64

Liver damage, think of first pass effect, especially in toxic doses.

Question 65

3 "R"s in Assay Development

Answer 65

-Robustness(obviousness) -Relaibility -Relevance

Question 66

Is biochemical assay target or phenotype based?

Answer 66

Target-based

Question 67

Is cell-based assay target or phenotype based?

Answer 67

Phenotype-based

Question 68

Emission of light during a chemical reaction that does not produce a significant quantity of heat

Answer 68

Chemiluminescence

Question 69

Production and emission of light by living organism (Lightning bugs)

Answer 69

Bioluminescence

Question 70

Goal of assay

Answer 70

To develop a kind of assay that best encompasses the function of the target in the cell