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Genetics - Block 2 > Human Gene Transcription > Flashcards

Human Gene Transcription Flashcards

1
Q

What does every gene require for activation of transcription by RNA polymerase II?

A

→ Nonspecific proteins and elements (DNA sequences)

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2
Q

How is transcription activated at the right time and right place?

A

→ Specific proteins and elements

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3
Q

What transcription factor phosphorylates RNA polymerase II in the PIC?

A

TFIIH

  • also has helicase activity
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4
Q

True or False

Most of the general transcription factors interact with the DNA?

A

False

GTF interact with themselves, not with DNA

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5
Q

What are the two things that bind to the DNA

A

Transactivators - bind regulatory sequence on DNA

TBD - binds to TATA box

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6
Q

Name the General Transcription Factors (GTF)

What are their functions?

A

TBP (subunit of TFIID) → Binds TATA box

TAFs (subunits of TFIID) → Bind sequence-specific transactivators

TFIIH → Provides a helicase activity for unwinding DNA (requires ATP) and phosphorylates the CTD of RNA pol II, thus initiating RNA synthesis

RNA polymerase II → synthesizes DNA

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7
Q

All of the following are examples of general transcription factors except for which ones?

TAF’s

TFIID

TFIIH

TBP

RNA polymerase II

Transactivators

A

Transactivators

  • bind to specific regulatory regions on the DNA
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8
Q

A viral infection results in the release of cytokines throughout the body. These cytokines bind with the cells of the body and lead to changes in gene expression and subsequently protein production in those cells. This is an example of:

A. Bacterial regulation of transcription

B. Inducible regulation of transcription.

C. Developmental regulation of transcription.

D. Transposon regulation of transcription

A

B. Inducible regulation of transcription.

The virus is inducing a change in transcription

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9
Q

What do co-activators recruit?

What do co-repressors recruit?

A

HATS

HDACS

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10
Q

Transactivators can directly bind to?

A

HATS

TAFS

Coactivators

Regulatory element

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11
Q

During development, one parent cell can result in daughter cells with different gene expression levels due to what?

A

Asymmetric distribution of transactivators in the parent cell so that each daughter cell winds up with different amounts of different transactivators

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12
Q

Congenital cardiac abnormalities typically show high amounts of mutations in which genes?

A

TBX1 and TBX5

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13
Q

What is the main reason for having a transactivator?

A

To induce transcription of certain genes to make certain proteins

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14
Q

At which point will transcription automatically occur?

A

Once the PIC forms, bringing in RNA polymerase II.

RNA Polymerase II is needed to go through transcription

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15
Q

Which of the following are regulated in development by transactivators?

Morphological differences

Biochemical differences

Both

Neither

A

Both Morphological differences Biochemical differences

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16
Q

True or False

NFKB is a transactivator?

A

True

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17
Q

In the NFKB signaling pathway, is removed from NFKB via .

A

IKB

phosphorylation

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18
Q

What do Nonspecific proteins do?

A
  • Include RNA polymerase II
  • Facilitate positioning RNA pol II to the proper start site for transcription.
  • Assemble at the TATA box.
  • Function in all RNA pol II promoters.
  • Are represented by the nomenclature, TFIIX, where X can be any of A-H, each a different protein.

The “TF” refers to transcription factor; “II” refers to RNA pol II.

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19
Q

Regulation of eukaryotic transcription can be what?

A

Developmental

→ transcription of different genes in different tissues or at different developmental stages

Inducible

→ transcription of genes in r_esponse to a hormone_

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20
Q

Basic elements for (specific!) developmental and inducible regulation of transcription:

A
  • “Genes” contain regulatory (or response) elements, which are short, specific sequences of DNA that bind specific proteins.
  • The specific proteins that are able to bind regulatory elements can activate or repress transcription. The proteins that activate transcription are referred to as transcriptional activators or transactivators.
  • The response elements are generally located 100-300 base pairs upstream or downstream of the TATA box.
  • A set of genes regulated in concert contain similar response elements
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21
Q

TFIID contains two subunits, what are they?

A

TAFS

TBP

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22
Q

Transactivators bind to their __________ , located among the regulatory elements of genes, after being activated by a certain inducer or at a certain stage in tissue development

→ _______________ recruit the TAFs of TFIID, leading to the binding of the TFIID complex to the TATA box.

→ TFIID binding to the TATA box leads to formation of the complete PIC and __________.

A

Regulatory regions

Transactivators

Transcription

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23
Q

Name a few ways you can stabilize PIC

A

Transactivator-TAF interactions

(direct or indirect), for stabilizing the PIC

TATA-TBP binding

Histone post-translational modifications

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24
Q

Protein Synthesis

A

aka Simple Synthesis

transactivators simply synthesized on the ribosome

they are good to go (transport process to the nucleus and either

  • reunite PIC interaction w/ TAF

or

  • recruit his tone acetyl transfer
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25
Covalent Modification
Covalent Modification (Phosphorylation) —\> phosphorylation that will change the polypeptide and its ready to go into the nucleus and find its binding site
26
Addition of Second subunit
Common in development common for 2 polypeptides to come together and make a sequence-specific transactivator
27
Unmasking
Having an inhibitor to prevent the transactivator from moving to the nucleus important in medicine An example will have phosphorylation of inhibitor so it goes away and gets degraded - Polypeptide doing the work (recruiting the PIC) is free to go into the nucleus and find a binding site
28
**Transactivators in development**
- Expression and asymmetric distribution to daughter cells - Endpoints have a clear connection to medical issues Key point: End up with asymmetric division of the actual proteins that go to one side of the cell or the other —\> one daughter cell or other daughter cell gets different sets of the transactivator
29
What are some examples of transactivators in development?
**Globin switching** **Heart morphology**
30
Transactivators and transcriptional regulation establish (morphology) pattern formation : If the regulation of transcription is off then what happens to the pattern and morphology?
The pattern is off and morphology can be off as well
31
Adult transactivators, synthesized later in development, bind what?
the adult globin gene regulatory elements
32
What is the basis for the hereditary persistence of fetal hemoglobin?
- Fetal cells will express a different transactivator in development the cells to that fetal hemoglobin transactivator would be earlier stage stem cells
33
T-box transcription factors and their roles in regulatory hierarchies in the developing heart
- T-box transcription factors are important players in the molecular circuitry that generates lineage diversity and form in the developing embryo. - At least seven family members are expressed in the developing mammalian heart _- TBX are transactivators_ The human T-box genes → TBX1 and TBX5 are mutated in cardiac congenital anomaly syndromes
34
Name the 5 examples of the Inducible regulation of transcription aka → signal transduction pathways
NFK STAT Basal Cell Carcinoma Ras Protein & GTP exchange factor FGF receptor mutations
35
**NFKB** Name the key points and key players for the NFKB pathway
**NFKB** → leads to activation of transactivator and transcription NFKB is a _transactivator_ **IKB** —\> inhibitory subunit that retains NFKB in the cytoplasm **TNF Alpha** —\> (reduces inflammation & autoimmunity) important signaling molecule in the immune system When its time for NFKB to be activated —\> IKB is phosphorylation When IKB is phosphorylation it gets degraded and leaves NFKB NKB is now free to go to the nucleus and bind its site and stimulate transcription **NFKB** is very important for _activation in many immune cells_ **TNF alpha —**\> if TNF doesn't bind to receptor = NFKB is blocked Therapy —\> blocks TNF alpha
36
**JAK STAT-1** Name the key points and key players for the STAT pathway
**STAT-1**→ leads to activation of transactivator and transcription A peptide that is interacting with the receptor brings two monomers together - on the inside of membrane —\> two kinases interacting with receptor polypeptide are close enough to activate each other Once activated —\> they add an additional phosphate group to the receptor That recruits STAT and gets phosphorylated In order to move into the nucleus —\> STAT gets phosphorylated - phosphate group should be a hindrance BUT - Phosphate groups bring two groups together (dimerization) and get buried and those charges get neutralized \*Important for **interferons** and big players in immunology Interferon signaling depends on STAT
37
**Hedgehog Pathway** Name the key points and key players for the Basal cell carcinoma pathway
**Hedgehog pathway has 2 outcomes:** 1. **Proliferation** --\> Hedgehog Signal 2. **No Proliferation** --\> No Hedgehog Signal _Normally_ • No Hedgehog Signal • Patched = inhibit smoothened • Smoothened inhibited = no interaction w/ protease • Not interacting with protease - Protease is free to cleave CI protein • Protease cleaves CI Protein = exposes corepressor • Co repressor enters nucleus & repress pro proliferation gene **= we do not get proliferation** If we _do want proliferation_ (by we cut ourselves) • Hedgehog signal on • Hedgehog will bind to patched and internalize parched • Patched = no longer inhibiting smoothened • Smoothened = free to interact with protease • Protease = no longer interact or cleave with CI protein • - CI protein fully intact • Express coactivator • **activate transcription or pro proliferated genes = gives us proliferation** 80% basal cell carcinoma due to dramatic mutations in patched Patched --\> receptor for hedgehog sitting in membrane Smoothened --\> n cytosine hanging on to patch below the membrane CI Protein —\> Transactivator
38
Name the key points and key players for the **Ras** ## Footnote **pathway**
2 receptors brought together and phosphorylate each other • Receptor have own kinase ability • Phosphorylation of receptos activates RAS GEF (GTP exchange factor) • Inactive RAS protein due to GDP binding • RAS GEF activated will exchange GDP for GTP and activate RAS protein • Get downstream signaling from there **Ras pathway = related to melanoma**
39
**FGF** **Pathway** Name the key points and key players for the FGF pathway
_Occurs in:_ - spermatocyte development - Development of chondrocytes **Fibroblast growth factor (FGF) receptor mutations** 1. Activating FGF mutations lead to INCREASED GROWTH of spermatocytes, ie, as men age, and thereby acquire more FGF mutations, more spermatocytes with those mutations, and therefore more sperm, HAVE FGF receptor mutations. 2. By contrast, FGF mutations in offspring lead to achondroplasia → shorten bone lengths, bc FGF receptor mutations INHIBIT chondrocyte division (for reasons that are not fully understood) = Develop **Achondroplasia (**shortened limbs in human, aka dwarfism) Inhibiting chondrocyte development --\> no growth in limbs = bad FGF is a mutation in the FGF receptor - very common as men age - Mutations cause their own expansion in cells
40
An extracellular signal, such as a peptide hormone in the blood, can lead to a change in the conformation of a \_\_\_\_\_\_\_\_\_\_\_\_, and subsequently, in the way, a series of cytoplasmic and nuclear proteins interact with one another. These changes ultimately lead to \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_, thus “transducing” the extra-cellular signal to the\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_.
**Receptor** **Signal transduction** **nucleus**
41
**DNA microarrays for determining levels of mRNA expression**
determine which RNA are present in a sample A single oligonucleotide hybridized to a nucleotide sequence derived from a sample that is being analyzed Fluorescence has to detect so we use **reverse transcriptase**
42
Specific and nonspecific factors and DNA sequences contribute to RNA polymerase II (RNA pol II) \_\_\_\_\_\_\_\_\_\_\_\_\_regulation in eukaryotes.
**Transcription**
43
The ____________ forms by an ordered assembly of components. Most of the components assemble by contacting other proteins of the PIC, not by contacting DNA. RNA pol II elongation proceeds by __________ of the RNA pol II by TFIIH.
**PIC** **Phosphorylation**
44
Specific activation of transcription is due to specific DNA sequences that bind specific regulatory factors, referred to as transcriptional activators or transactivators. The transactivators bind to components of the \_\_\_\_\_\_\_\_\_\_, especially the TATA binding protein (TBP) associated factors (TAFs), facilitating the formation of the PIC. Transactivators can also make \_\_\_\_\_\_\_\_\_\_\_\_\_more accessible.
**TFIID** **Chromatin**
45
The activation of the ____________ is regulated by various biochemical mechanisms that either prevent or allow binding of the transactivator to its \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_.
**Transactivator** **Regulatory element**
46
Transactivators have two distinct \_\_\_\_\_\_\_\_\_\_\_\_: A transactivation domain, that contacts components of the PIC, especially the TAFs; and a __________ domain that binds a specific regulatory element.
**Domains** **DNA binding protein**
47
Transactivators regulate _____________ biochemical and pattern-formation phenotypes, that is, aspects of development.
**Developmental**
48
\_\_\_\_\_\_\_\_\_\_\_\_\_signals are ________________ via intracellular activation of a transactivator, leading to the transcriptional activation of a subset of genes. There are a variety of transactivator activation mechanisms, with STAT1 and NF-kappaB representing two distinct examples.
**Extracellular** **transduced**
49
Because the entire ___________ has been sequenced, __________ and developmental regulation of a transcriptome can be determined.
**Genome** **Inducible**
50
Because many mammalian genomes have been completely sequenced, transcriptional ____________ can be identified by evolutionary _____________ of DNA sequences.
**Activator** **Conservation**
51
\_\_\_\_\_\_\_\_\_\_\_\_\_ can facilitate promoter reactivation, for example, fetal globin gene activation.
**HDAC inhibitors**
52
Sickle cell anemia is being treated by reactivation of the \_\_\_\_\_\_\_\_\_\_\_\_by HDAC inhibitors. The low-level expression of the fetal globin protein disrupts polymer formation caused by presence of the mutated adult globin gene.
**Fetal Hemoglobin Gene**
53
Many human diseases are caused by defects in either ___________ or transcriptional regulatory proteins
**Transcription binding sites**
54
HPFH is caused by a mutation in the ________ regulatory elements, allowing binding of the adult globin transactivator to the fetal globin \_\_\_\_\_\_\_\_.
**Transcriptional** **Gene**
55
Mutations in the FGF receptor are responsible for \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_, in turn traceable to the accumulation of FGF receptor mutations in the sperm of older men, in turn tracealeto the _________ effects of these FGF receptor mutations for sperm pre-cursor cells.
**Achondroplasia** **Increased growth effects**
56
Transcriptional repression can occur by repressor blockage of a \_\_\_\_\_\_\_\_\_\_\_\_, by the repressor binding to that site.
**Transactivator binding site**
57
HDACs can lead to the generation of methylated DNA by de-acetylating histones, which leads to histone methylation, which leads to the binding of \_\_\_\_\_\_\_\_\_\_\_, which leads to the binding of DNMTs, which methylate cytosines.
**HP-1**
58
\_\_\_\_\_\_\_ is the phenomenon of heritable changes in the genome that do not involve mutations. Epigenetic mechanisms usually involve the maintenance of inaccessible _________ over many cell divisions.
**Epigenetics** **Chromatin**
59
60
Certain histone\_\_\_\_\_\_\_\_\_\_\_\_\_lead to the binding of HP-1 to the histones and the condensation of chromatin. The term\_\_\_\_\_\_\_\_\_\_\_ refers to post-translational modifications of histones which can lead to the interaction of histones with different proteins that will either repress or active transcription.
**Post-translational modifications** **Histone Code**
61
In the case of the inactive, mammalian female X chromosome, _________ tethers chromatin-modifying proteins to the chromatin to ensure heterochromatin spreading throughout, and methylation of this chromosome. \_\_\_\_\_\_is epigenetics over a generation rather than from parent to daughter cell. Only a very small fraction of human genes are subject to imprinting.
**XiSt RNA** **Imprinting**
62
is due to a defect in the imprinting process for a particular set of genes.
**Prader-Willi syndrome**
63
DNA \_\_\_\_\_\_\_\_\_\_\_are present at the replication fork and are the enzymes that catalyze DNA methylation. Only _______ is methylated in mammals. \_\_\_\_\_\_\_\_\_\_\_bind methyl-cytosines and also bind HDACs, leading to methylation of histones
**Methyltransferase** **Cytosine** **MBPs**
64
True or False Domain: a portion of a polypeptide Polypeptide: 1 Polypeptide Protein: Multiple polypeptides
True
65

Genetics - Block 2 (1 decks)

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