Chapter 12 (Part 2)
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What genes do RNA Polymerase 1 transcribe?
All genes that encode rRNA except 5s rRNA.
What does RNA Polymerase 2 transcribe?
How many subunits does it have?
- Transcribes all structural genes and certain snRNA genes needed for pre-mRNA splicing.
- Responsible for the synthesis of all mRNA.
- 12 sub units
What genes does RNA polymerase 3 transcribe?
All tRNA and 5s rRNA genes.
What is basal transcription?
A minimal rate that a core promoter can produce a low level of transcription.
What is a core promoter made up of?
- Tansitional start site
- TATA box
Where is the regulatory element located at?
-100 through -50
Where is the TATA box located?
What are the two categories of regulatory elements and what do each of them do?
- Enhancers (Stimulate transcription)
- Silencers (Inhibit transcription)
What are the three categories of proteins are needed for basal transcription at the core promoter?
- RNA polymerase 2
- General transcription factors
- Mediator (protein complex)
What is the largest of all the transcription factors?
What recognizes the TATA box in the preinitiation complex?
What two transcription factos bind to TF2D?
What is the function of TF2 A&B?
Enable RNA polymerase two to bind to the core promoter by a linkage of TF2F binding to A&B.
What two transcription factors bind to RNA polymerase two?
What is the function of TF2 H&E?
They act as a helicase to form the open site.
What is the structure of the mediator in the preinitiation complex?
- A large protein complex.
- The core subunits form an elliptical-shaped complex that partially wraps around RNA polymerase two.
What is the function of the mediator in the preinitiation complex?
- Mediates interactions between RNA polymerase two and regulatory transcription factors that bind to enhancers and silencers.
- Regulates the ability of TF2H to phosphorylate the CTD.
What is the first mechanism used to alter chromatin structure?
Amino terminal ends of histone proteins can be covalently modified in a variety of ways including acetylation of lysine, methylation of lysine, and phosphorylation of serine.
What is caused by the acetylation of lysine in the first mecahnism used to alternation of chromatin structure?
Residues at the N terminus of histone proteins removes positive charges, thereby reducing the affinity between histones and DNA.
The second mechanism used in alteration of chromatin structure is also called what?
ATP dependent chromatin remodeling.
Describe the second mechanism of alteration of chromatin structure.
Energy of ATP hydrolysis is used to drive a change in the structure of the nucleosomes making DNA more accesible for transcription by shifting or changing the spacing between nucleosomes.
What is the function of the SWI/SNF protein family found in all eukaryotes?
Catalyze ATP dependent chromatin remodeling.
What is Colinearity?
The one to one correspondence between the sequence of codons in DNA coding strand and the amino acid sequence of the polypeptide.
What is RNA splicing?
During transcription, an RNA is made corresponding to the entire gene sequence. Subsequently, the sequences in the RNA that correspond to the introns are removed, while the RNA sequences derived from the exons are connected (spiced).
How is mature tRNA made in the cell?
Precursor tRNA contains tRNA molecules in a long strand that must be cut out by exonucleases.
Describe the excision of group 1 & 2 introns.
Introns that excise themselves from immature RNA and catalyzes the joining of flanking exons. No ATP is required.
What is the function of Maturases?
Enhance the rate of splicing.
Describe the method of which Group 1 & 2 introns are removed and joined together.
- Group 1 : external G initiates splicing.
- Group 2 : internal A initiates splicing. (Forms a lariat structure with the internal A.)
What is another name for Pre-mRNA?
- Heterogeneous Nuclear RNA
Describe hnRNA splicing.
- Must be altered before leaving the nucleus.
- Not self-splicing; requires aid of a splicosome.
What is a Splicosome?
- Composed of several subunits known as snRNPs that contain small nuclear RNA and a set of proteins.
- Found only in the nucleus.
What is alternative splicing (Intron advantage)?
Allows deifferent variation of exons being included or excluded in an mRNA sequence allowing us to have multiple proteins from one gene. Which allows us to carry fewer genes.
What is capping?
At their 5' end, most mature mRNA have a 7-methylguanosine covalently attached.
_____ is needed for the proper exit of certain RNAs from the nucleus?
What do most mature mRNA have attached at the 3' end?
Why is it important?
- A string of Adenine nucleotides.
- This increases the stability of mRNA and the translation of polypeptides.
Where will endonucleases cut to attach the poly A tail?
within 20 nucleotides of the consensus site.
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