Term
| What experiment proved that eukaryotic cells contain all the genetic instructions to form a complete organism? |
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Definition
| Frog skin cell DNA was injected into an egg, leading to a normal embryo |
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Term
| What is the main difference between prokaryotic and eukaryotic transcription/translation? |
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Definition
| Prokaryotic transcription/translation is coupled, eukaryotic is separated by space and time |
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Term
| What are the two main ways gene expression can be regulated at the transcription level in eukaryotes? |
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Definition
1. Modifying chromatin structure
2. Controlling activity of RNA polymerase |
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Term
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Definition
| Won Nobel Prize in Chemistry in 2006 for discovering nucleosome, dozens of proteins needed for transcription, Mediator complex, enhancers, and structure of RNA polymerase |
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Term
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Definition
| Contains an initiator (Inr) and a TATA box; location +1 |
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Term
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Definition
Upstream activator sequences in yeast
Two or more often work together and depend on spacing |
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Term
| Give an example of a UAS/enhancer |
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Definition
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Term
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Definition
| Like a UAS, but in higher eukaryotes
Located at variable places, usually far
Work as an enhancer or silencer |
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Term
| How is bacterial polymerase different from eukaryotic polymerase? |
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Definition
| Eukaryotic polymerase is larger, has more than 10 subunits |
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Term
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Definition
| A C-terminal domain on poly II that is regulated via phosphorylation |
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Term
| What is required for eukaryotic polymerase to bind to its core promoter element and initiate synthesis? |
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Definition
1. Assistance from a set of 6 eukaryotic factors
2. ATP hydrolysis and a conformation change |
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Term
| What is the function of TFIID? |
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Definition
| It is a DNA sequence-specific DNA binding protein that binds to the core promoter element and recruits RNA polymerase and the remaining general initiation factors |
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Term
| What within TFIID binds the TATA box? |
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Definition
| The TATA-box-binding protein (TBP) |
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Term
| What within TFIID binds the DNA initiator element? |
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Definition
| TBP-associated factors (TAFs) |
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Term
| What is the function of TFIIA? |
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Definition
| It stabilizes binding of TFIIB and TBP to the promoter |
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Term
| What is the function of TFIIB? |
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Definition
| It recruits polymerase to the promoter |
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Term
| What is the function of TFIIF? |
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Definition
It stabilizes binding of RNA polymerase to TFIID and TFIID
It is also required for entry of TFIIE and TFIIH |
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Term
| What is the function of TFIIE? |
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Definition
| It is a heterodimeric protein required, along with TFIIH, to promote ATP-dependent formation of the open complex |
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Term
| What is the function of TFIIH? |
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Definition
Along with TFIIE it promotes ATP-dependent formation of the open complex with helicase activity
It also has a kinase activity for CTD tail phosphorylation |
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Term
| What is the function of transcription factor Sp1? |
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Definition
| Sp1 (the GC box) is for constitutive regulation of many pol II grades |
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Term
| What is the function of transcription factor CTF? |
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Definition
CTF (the CCAAT box) is for constitutive regulation of many pol II genes
Plays a strong role in efficiency, but does not influence specificity |
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Term
| What is the function of transcription factor HSTF? |
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Definition
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Term
| What is the function of transcription factor CREB? |
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Definition
Regulation of cAMP responsive genes
(seen in lac operon, for example) |
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Term
| What is the function of transcription factor glucocorticoids, mineralocorticoids, and progesterone receptors? |
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Definition
| Regulation of steroid-responsive genes |
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Term
| Describe properties of Group A steroid receptors |
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Definition
1. Large A/B regions
2. Associated with heat shock proteins
3. Doesn't bind DNA until ligand binds
4. Dimerizes and binds as homodimers
5. Bind to similar consensus sequences |
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Term
| Describe properties of Group B steroid receptors |
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Definition
1. Short A/B receptors
2. Nuclear receptors
3. NOT associated with heat shock
4. Bind DNA in absence of ligand
5. Silence genes
6. Heterodimerize
7. Bind to the exact same consensus sequence |
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Term
| How is steroid receptor binding to DNA regulated? |
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Definition
| Hormone response element binding occurs via zinc fingers with two 5 amino acid sequences (P box and D-box) that controls binding |
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Term
| Define co-factors and their role in steroid receptors |
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Definition
| They are required for steroid receptor activation of target genes via a "higher order" complex |
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Term
| What criteria must a factor meet to be called a "co-activator"? |
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Definition
1. It must be a limiting factor (ie, there's not enough to bind every receptor)
2. Must make protein-protein contact, not bind DNA directly
3. Ligand binding regulates co-activator interaction with the receptor |
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Term
| What is the function of a "co-repressor"? |
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Definition
| To repress basal transcription of genes when they bind DNA without hormone |
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Term
| Give two examples of Group A steroid receptors |
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Definition
| Estrogen receptor, androgen receptor |
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Term
| Give two examples of Group B steroid receptors |
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Definition
| Thyroid receptor, Vitamin D receptor |
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Term
| What are the three classes of DNA binding transcriptional regulator motifs? |
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Definition
1. Helix-turn-helix
2. Zinc finger
3. Leucine zipper |
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Term
| Describe the helix-turn-helix motif |
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Definition
The most common DNA binding domain in prokaryotic regulatory proteins, binds DNA in the major groove
Often present on proteins that bind DNA as dimers (ex. the trp repressor) |
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Term
| Describe the zinc finger motif |
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Definition
| Found mainly in eukaryotic regulatory proteins (ex. estrogen receptor, glucocortocoid receptor) |
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Term
| Describe the leucine zipper motif |
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Definition
Found in eukaryotic proteins, the leucine areas are hydrophobic and bind like a zipper
The DNA binding domain is two alpha helixes with high leucine and argenine
Doesn't bind DNA directly, mediates protein-protein interaction |
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Term
| Describe the size of a chromosome and how much DNA must fit in |
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Definition
| 5-8 micrometers in diameter but must fit 2 meters of DNA, so VERY compact |
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Term
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Definition
| A complex of protein and DNA to make it compact |
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Term
| Does chromatin exist in prokaryotes? |
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Definition
| No, because the default state for most prokaryotic genes is "on" |
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Term
| Define the nucleosome core |
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Definition
| 146bp of DNA wrapped 1.75 turns around a histone core |
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Term
| Describe the histone core |
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Definition
| 8 molecules of histone proteins |
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Term
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Definition
| 166bp of DNA wrapped 2 turns around a histone core (actually binds to one of the histone proteins) |
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Term
| Define repeating nucleosome unit |
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Definition
| A nucleosome (DNA wrapped around a histone) with linker DNA connected to the next unit |
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Term
| What amino acids do histones have a high proportion of, and why? |
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Definition
| They have high amounts of Lysine and Arginine, to neutralize the negative DNA and bind tightly |
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Term
| Describe the levels of chromatin structure |
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Definition
1. DNA
2. "Beads on a string"
3. Fiber
4. Loop
5. Rosette (six loops)
6. Coil (six rosettes)
7. Chromatid (ten coils) |
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Term
| What modifying activities can happen to a chromatin at rest? |
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Definition
| It is restricted at rest, but can be silenced or activated by modifying proteins |
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Term
| How can histones be modified to initiate transcription? |
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Definition
Acetylation of the lysine residues: this neutralizes charge (loosening DNA) and acts as a signal for other proteins)
Carried out by histone acetyl transferase (HAT) |
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Term
| What enzyme acetylates lysine in histone? |
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Definition
| Histone acetyl transferase (HAT) |
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Term
| What area on a transcription factor interacts with acetylated histones? |
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Definition
The bromodomain
(sounds like a frat house) |
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Term
| How do chromatin-remodeling enzymes initiate chromatin remodeling? |
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Definition
| The chromatin-remodeling engines utilize energy from ATP hydrolysis to shift the positions of nucleosomes along the DNA and to induce other conformational changes in chromatin. |
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Term
| What causes Burkitt's Lymphoma? |
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Definition
The c-myc gene encodes transcription-activating protein
In the disease, c-myc is relocated to an area of the chromosome close to the immunoglobulin (Ig) gene
As a result, it is constantly stimulated, leading to over-proliferation of B-cells and lymphoma |
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Term
| How does c-Myc protein activate transcription? |
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Definition
It binds DNA (through the E box element) and interacts with factors such as TRAAP
TRAAP causes histone acetylation and therefore transcription |
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Term
| What is the transcriptional inhibitory protein analogous to c-Myc? |
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Definition
| Mad protein (which binds to the same E box element, but causes histone deacetylation) |
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Term
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Definition
It binds to the same ligand-binding site in the estrogen receptor that estrogen binds, preventing recruiting of coactivator
This inhibits the growth of estrogen-depending breast tumors |
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