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41 Cards in this Set
- Front
- Back
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What happens during eukaryotic transcription
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-RNA polymerase II transcribes protein coding genes
-Requires five general transcription factors' TFIID, TFIIB, TFIIF, TFIIE, and TFIIH (prokaryotes only need one; σ factor) -Eukaryotic genes lack operons -Eukaryotic DNA is packaged into chromatin which provides an additional mode of regulation -Eukaryotic transcriptional activation requires many gene regulatory proteins |
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What does RNA polymerase II do?
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In Eukaryotic transcription it transcribes protein coding genes
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What five general transription factors does Eukaryotic transcription require?
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TFIID, TFIIB, TFIIF, TFIIE, and TFIIH (prokaryotes only need one; σ factor)
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What general transcription factor does prokaryotic transciption require?
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σ factor
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Do Eukaryotic genomes have operons?
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no
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What is Eukaryotic DNA packaged into?
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chromatin which provides an additional mode of regulation
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In Eukaryotic transcription what does the mediator do?
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It acts as an intermediate between regulatory proteins and RNA polymerase
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What is Eukaryotic gene expression controlled by?
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by many regulatory proteins (~2000 encoded by the human genome) both activators and repressor
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Can gene regulatory proteins in eukaryotic gene regulation act over large distances?
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yes, can act over very large distances, sometimes >10000 base pairs away
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in eukaryotic gene regulation how do gene regulatory proteins act over large distances?
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one way is through DNA looping
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what do eukaryotic gene regulatory proteins often function as
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as protein complexes on DNA
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in eukaryotic gene regulation where do coactivators ans corepressors assemble?
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on DNA-bound gene regulatory proteins, they do not directly bind DNA
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in eukaryotic gene regulation what is the modular design of eukaryotic activator proteins
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1) DNA binding domain (BD)
- recognizes specific DNA sequences 2) Activation domain (AD) - accelerates rate of transcription |
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in eukaryotic gene regulation what does the DNA binding domain (BD) do?
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it is part of Eukaryotic Activator Proteins which recognizes specific DNA sequence
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in eukaryotic gene regulation what does the Activation domain (AD) do?
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it is part of Eukaryotic Activator Proteins which accelerates rate of transcription
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in eukaryotic gene regulation can you mix DB and ADs
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yes
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in eukaryotic gene regulation how do activator proteins activate transcription
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they attract, position and modify;
general transcription factors mediator RNA polymerase II They can do this either: 1) Directly by acting on these components 2) Indirectly modifying chromatin structure |
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In Eukaryotic Gene Regulation what do activator proteins bind to as one of the ways to activate transcription
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they can bind directly to transcriptional machinery or mediator and attract them to promoters (like porkaryotic activators)
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In Eukaryotic Gene Regulation what can activator porteins alter as one of the ways to activate transcription
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they can alter chromatin structure
Nucleosomes are the basic structure of Eukaryotic chromatin -DNA wound around a histone octamer (H2A, H2B, H3, and H4 X2) |
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what are the basic structure of Eukaryotic chromatin
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Nucleosomes
-DNA wound around a histone octamer (H2A, H2B, H3, and H4 X2) |
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in eukaryotic gene regulation how do nucleosomes pack
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they pack as compact chromatin fibers
transcriptional machineray cannot assemble on promoter tightly packaged in chromatin activator porteins can alter chromatin structure and increase promoter accessibility |
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in eukaryotic gene regulation can transcription machinery assemble on promter
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no, the promoters are tightly packaged in chromatin
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can activator proteins alter chromatin structure
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yes which increases promoter accessibility
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in eukaryotic gene regulation how many major ways can activator proteins alter chromatin
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4
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in eukaryotic gene regulation how can nucleosome structure be altered
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by chromatin remodeling complees in an ATP-dependent manner to increase promoter accessibility
-nucleosome sliding |
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in eukaryotic gene regulation what is required for nucleosome removal and histone exchange
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it requires cooperation with histone chaperones
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in eukaryotic gene regulation what is the histone code
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it is when histone modifying enzymes produce specific patterns of histone modifications
addition of phosphate group: - phosphorylation - enzyme: kinase addition of acetyle group: - acetylation - enzyme: acetyl transferase addition of methyl group: - methylation - enzyme: methyl transferase histone modification can occur on specific amino acids of histone tails |
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in the histone code of eukaryotic gene regulation, what enzyme is used and what is called for the addition of phospate group, acetyl group and methyl group
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addition of phosphate group:
- phosphorylation - enzyme: kinase addition of acetyle group: - acetylation - enzyme: acetyl transferase addition of methyl group: - methylation - enzyme: methyl transferase |
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in the histone code of eukaryotic gene regulation where can histone modification occur
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they can occur on specific amino acids of histone tails
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in the histone code of eukaryotic gene regulation what are writers
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an histone modifying enzymes which does specific modifications to histone tails
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in the histone code of eukaryotic gene regulation what are readers
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they are proteins that can recognize specific modification and provide meaning to the code
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in eukaryotic gene regulation what is an example of transcriptional regulation using the histone code
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human interferon gene promoter
step 1: activator protein binds to chromatin DNA and attracts a histone acetyl transferase (HAT) step 2: HA acetylates lysine 9 of histone H3 and lysine 8 of histone H4 step 3: activator portein attracts a histone kinase (HK) step 4: HK phosphorylates serine 10 of histone H3. Can only occur after acetylation of lysine 9 Step 5: Serine modification signals the acetyltransferase to acetylate lysine 14 of histone H3 histone code for transcription intiation is written step 6: TFIID and a chromatin remodelling complex bind to acetylated histone tails and initiate transcription |
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what is the human interferon gene promoter and how does it work
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it is a part of eukaryotic gene regulation
it is an example of transcriptional regulation using the histone code step 1: activator protein binds to chromatin DNA and attracts a histone acetyl transferase (HAT) step 2: HA acetylates lysine 9 of histone H3 and lysine 8 of histone H4 step 3: activator portein attracts a histone kinase (HK) step 4: HK phosphorylates serine 10 of histone H3. Can only occur after acetylation of lysine 9 Step 5: Serine modification signals the acetyltransferase to acetylate lysine 14 of histone H3 histone code for transcription intiation is written step 6: TFIID and a chromatin remodelling complex bind to acetylated histone tails and initiate transcription |
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in eukaryotic gene regulation how does transcription repression work
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unlike prokaryotes, eukaryotic repressor proteins rarely compete with RNA polymerase for access to DNA
instead use a variety of mechanisms to inhibit transcription |
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in eukaryotic gene regulation what mechanisms are used to inhibit transcription
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interfering with activator function
- competitve DNA binding - masking the activation surface - direct interaction with the general transcription factors by altering chromatin structure - recruitment of chromatin remodeling complexes by altering histone code - recruitment of histone deacetylases - recruitement of histone methyl transferase |
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guided by gene regulatory proteins what can histone "reader" and "writer" proteins establish?
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they can establish a repressive form of chromatin
histone code can spread theis chromatin can be stabilized |
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in eukaryotic gene regulation how is the spreading of the histone code along chromatin carried out
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it is carried out by reader-writer complexes
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in eukaryotic gene regulation how do reader-writer complexes work?
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DNA methylase enzyme is attracted by Reader and methylates nearby cytosines in DNA
DNA methyl-binding proteins bind methyl groups and stabilize structure -methylation and therefore gene expression patterns can be inherited, a process called epigentic inheritance |
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what is epigenetic inheritance
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it is the ability of a daughter cell to retain memory of the parental gene expression pattern without modifying the DNA sequence
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what is a DNA microarray
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it helps with transcriptome anaylyses
part of analysis of a large set of cellular transcripts it provides a "signature" of cell type |
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in transcriptome analyses what do microarray provides a "signature" of cell state;
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response to extracellular stimuli
disease states eg cancer |
