Exam 4

Question 1

Define/describe proto-oncogene

Answer 1

Normal gene, frequently linked to the regulation of cell proliferation; can be converted into an oncogene by overexpression or mutation

Question 2

Define/describe oncogene

Answer 2

A gene whose protein product can make cells cancerous when it is overexpressed or mutated

Question 3

Define/describe oncoprotein

Answer 3

Proteins encoded by oncogenes (dysregulated or activated genes) and have a potential to cause cancer

Question 4

Define/describe retroviruses

Answer 4

A retrovirus has an RNA genome; replicates by making an RNA-DNA hybrid and then double-stranded DNA which gets integrated into host chromosomes

Question 5

Define/describe transformation

Answer 5

The incorporation/transfer of viral/foreign DNA into host genome

Question 6

Define/describe double minute chromosomes

Answer 6

Typically seen in tumors/for specific oncogenes, regions of DNA amplification that result in overexpression

Question 7

Define/describe ErbA

Answer 7

• Nuclear receptor family of TFs (hormone-dependent transcription)
• Contains a region that can bind the thyroid hormone. After binding, the hormone-receptor complex induces transcription of thyroid hormone-responsive genes

Question 8

Define/describe trans-splicing

Answer 8

Splicing reaction between two RNA molecules encoded by different genes, can produce chimeric RNA encoding a fusion protein

Question 9

Define/describe tumor suppressor genes

Answer 9

• Genes that encode proteins involved in the inhibition of cell growth/division
• Also called anti-oncogenes or cancer preventers

Question 10

Define/describe retinoblastoma protein

Answer 10

• Rb-1
• First identified tumor suppressor
• Inhibits activation by TF E2F
• Recruits HDACs and histone methylases

Question 11

Define/describe wild-type

Answer 11

The “normal” allele or typical phenotype

Question 12

Define/describe quenching

Answer 12

• The blocking of activity
• Ex: Rb “quenches” E2F’s activity, keeping chromatin closed and resulting in no transcription

Question 13

Define/describe DNA tumor viruses

Answer 13

Viruses that encode proteins with oncogenic potential, disrupting normal cellular pathways

Question 14

Define/describe haploid insufficiency

Answer 14

A disease in which one copy of a gene is mutated and the remaining wild-type copy cannot produce sufficient functional protein to prevent disease

Question 15

Define/describe triplet repeat diseases

Answer 15

Diseases involving the abnormal amplification of a three base pair sequence

Question 16

Define/describe RAN translation

Answer 16

• Repeated associated non-AUG
• Repeats hinder initiation at AUG
• Abnormal proteins are produced

Question 17

Define/describe interferon

Answer 17

• A class of cytokines secreted by virus-infected cells and certain T cells
• Induce antiviral responses by activating JAK/STAT pathway to turn on antiviral genes (proteins and miRNAs)
• STAT heterodimer forms complex with IRF9 TF to run on target antiviral genes

Question 18

Define/describe BRD4

Answer 18

• Bromodomain protein
• BRD4-NUT oncogenic fusion protein produces abnormally enhanced histone acetylation and opening in the chromatin of genes associated with growth stimulation

Question 19

Define/describe designer zinc finger

Answer 19

• Can be used as a drug therapy to alter gene transcription
• Alpha helical region contacts DNA, allowing specific region of genome to be altered
• Designer zinc fingers can be used to switch expression ON or OFF

Question 20

Define/describe RNA interference (RNAi)

Answer 20

• Short RNA molecules which are complementary to a target mRNA can be produced and used to inhibit it post-transcriptionally
• Therapeutic procedures involving artificial inhibitory RNAs can involve small RNAs complementary to the target mRNA which bind to it and induce its degradation or block its translation. Alternatively it can involve longer RNAs which are complementary to it and will therefore bind to it producing a double-stranded RNA molecule. This molecule will be cleaved to produce siRNAs which can bind to further copies of the target mRNA and induce its degradation

Question 21

What mechanisms do the following oncoproteins use to regulate gene expression?
a. V-ErbA
b. Myc
c. MDM2, MDM4

Answer 21

A. v-ErbA: Dominant repressor, competes for binding with promoter. Blocks hormone dependent gene expression

B. Myc: Can stimulate gene expression in 3 ways: 1. heterodimerization with Max 2. heterodimerization with PTEF-b and 3. heterodimerization with TFIIH

C. MDM2: altering TF activity by promoting/inhibiting protein : protein interactions. Promotes p53 ubiquitination, but small molecule nutlin blocks p53 interaction, allowing p53 to still inhibit tumor growth.

Question 22

How would you cure a transcriptional disease?

Answer 22

• Could target chromatin modifying proteins
• Could target epigenetic modifications by targeting modification directly (azacytidine), inhibiting enzymes that produce modification (histone acetylases), inhibiting enzymes that remove modification (histone deacetylases), inhibit interactions of the modification with other factors (bromodomain : acetyl groups)
• Nucleic acid therapies
• Design zinc fingers to switch expression OFF or ON

Question 23

What type of factors that regulate gene expression can be mutated in human diseases?

Answer 23

• TFs
• BTC components
• CMCs
• Co-activators
• RNA processing

Question 24

Describe RAN translation details

Answer 24

The ribosome does not initiate translation at the normal AUG translation initiation codon. Rather it initiates translation within the CGG repeat sequence to produce polyglycine or polyalanine depending on whether translation takes place in the GGC or GCG reading frame

Question 25

Describe molecular details for all p53-linked functions

Answer 25

- p53 can interact with GIGs (genes whose proteins inhibit growth), inducing growth arrest - p53 can also interact with GSGs (genes whose proteins stimulate growth) through direct mechanisms and indirect mechanisms

Question 26

What general and/or specific genes are regulated by p53? What are p53’s tumor suppressor functions?

Answer 26

- p53 is a tumor suppressor that is involved in the activation of expression of genes that inhibit growth (can induce growth arrest) - Is considered a sensor of DNA damage - It is induced by DNA damage - Mutated in many cancers

Question 27

How do viruses manipulate gene expression?

Answer 27

- Degrade cellular RNAs - Decapping enzymes block cap-dependent translation - Have IRESs in viral mRNAs - Viral "cap" proteins to allow host cell ribosomes to translate uncapped viral transcripts

Question 28

How do retroviruses become tumorigenic?

Answer 28

The virus integrates next to proto-oncogene, followed by incorrect incision, resulting in cancer-causing virus carrying oncogene

Question 29

How can chromosome translocation result in a change in gene expression?

Answer 29

- It can put regulatory elements on chromosomes, resulting in higher levels of expression - It can result in the orientation of transcription being changed (head-to-head orientation // divergently transcribed), resulting in an increase in oncogene expression

Question 30

What are the 4 consequences of Jun binding to ccl2 gene?

Answer 30

- Histone phosphorylation - Histone acetylation - Recruitment of NFkB - Recruitment of RNAP II All result in increased transcription of ccl2 gene

Question 31

Leucine zippers promote...

Answer 31

Jun/Fos heterodimers

Question 32

Jun and Fos normally promote...

Answer 32

cellular growth via transcription of various genes

Question 33

Phosphorylation of Jun disrupts...

Answer 33

NuRD interactions

Question 34

Can v-ErbA bind thyroid hormone or activate transcription? How is v-ErbA oncogenic?

Answer 34

- Cannot bind TH or activate transcription - It is oncogenic because it is a dominant repressor and it blocks hormone-dependent gene expression

Question 35

Describe the v-ErbA inhibitory domain

Answer 35

- v-ErbA contains an inhibitory domain that recruits a co-repressor - The inhibitory domain is essential for transformation

Question 36

v-ErbA must do what to transform?

Answer 36

Repress transcription

Question 37

c-erbA is involved with the development of

Answer 37

RBCs

Question 38

What does v-erbA do?

Answer 38

Inhibits c-erbA, letting the blood cells to continue replicating

Question 39

What does v-ErbA encode that allows cells to grow without growth factor stimulation?

Answer 39

A truncated EGF receptor

Question 40

What are the three ways that Myc can stimulate gene expression?

Answer 40

- Myc can heterodimerize with Max, resulting in enhanced transcriptional initiation - Myc can heterodimerize with PTEF-b, resulting in enhanced transcriptional elongation - Myc can heterodimerize with TFIIH, stimulating the activity of GMT, resulting in enhanced translation

Question 41

What are the consequences of genome translocations?

Answer 41

- Gene overexpression - Oncogenic fusion proteins

Question 42

Describe the direct mechanisms by which p53 represses GSGs

Answer 42

- Compete for activator binding sites - Close chromatin - Bind up activators

Question 43

Describe the indirect mechanisms by which p53 represses GSGs

Answer 43

- p21 (inhibits cyclin-dependent kinases needed for growth; p21 is a growth arrest gene) - Turn on miRNAs - Turn on lncRNAs

Question 44

How is p53 regulated or thwarted?

Answer 44

- Deletion of the gene - Mutation - MDM2 overexpression

Question 45

Mutant p53 can bind...

Answer 45

- Alternative sequences in promoters that wt p53 won't - Other TFs

Question 46

What is MDM2?

Answer 46

An oncogenic protein that misdirects or inactivates p53 activity

Question 47

How can p53 evade MDM2?

Answer 47

Via acetylation, which inhibits MDM2 interaction and recruits TAF1 (TFIID component)