This is an interactive review sheet that encourages you to interact with the material and draw out the critical information.  There are several ways to contribute:

 

• Add an important vocabulary word and its definition to the list from a specific lecture.  These are anything you feel is essential to the understanding of the material including the names and functions of proteins, types of chemical bonds, names of processes, etc.

• Add an answer to one of the concept questions

• Edit and expand on another student's posting

• Add a link to another website, a video on You Tube, or any other teaching material on the web that you think enhances your understanding of the material.

 

As I stated in class, 8 points of your exam grade is dependent on your participation in this dialog about the material.  I will use the following rubric for grading: 3 points for adding and defining one vocabulary word, 3 points for participating in the answering of one of the concept questions, 2 points for editing and expanding on another student's posting (edits must be more than just removing a word or adding a word, it must have an impact on the material discussed)

 

Contributions to this review must be completed by 5 p.m. on April 21st (the Tuesday before the exam)

 

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Topic 14 Eukaryotic Transcription

 

Important Vocabulary:

TATA Box-A sequence of DNA (T,A,T,A,A/T,A,A/T) located in the promotor region of eukaryotic genes and recognized by TATA binding protein (TBP), one of the many transcription factors involved in eukaryotic transcription.

 

Important Concepts:

 

What are the different roles of Pol I, II, and III?

Pol I, Pol II, and Pol III are Polymerases. Pol I is located in the nucleolus and it transcribes 18S and 28S rRNA. Pol II makes mRNA and is found in the nucleus NOT the nucleolus. Pol III works on 5S rRNA, tRNA, and small non-coding RNA. Pol III is located in the nucleus NOT the nucleolus.

 

What are General Transcription Factors?

General transcription factors (GTFs) help polymerase II to recognize and bind with the promoter region of eukaryotic genes, and therefore, they play an active role in the initiation of eukaryotic transcription. The GTFs involved in the initiation stage are TFIIA, TFIIB, TFIID, TFIIE, TFIIF & TFIIH. Each GTF has a specific role in helping the polymerase II to recognize, bind, and begin transcription of the DNA strand. Many of the GTFs bind with polymerase II to form the preinitiation complex which is able to recognize and bind to the DNA template strand in order to form the closed complex. Some of the GTFs then help to "melt" the DNA, and TFIIH uses ATP to form a transcription bubble which begins the open phase of initiation and leads to the phosphorylation of the C-terminal domain.

 

What is the function of TFIID?

TFIID is protein that is made up of a complex of subunits, including the TATA binding protein (TBP). TFIID helps to position the polymerase II over the transcriptional promoter region. The TBP unit of the complex is what is responsible for identifying the promoter region since it specifically binds with the TATA box sequence located within the promoter. Without the TFIID, the polymerase is unable to recognize the promoter region, and therefore, transcription can not begin. The TBP also helps the DNA to "melt" during the formation of the transcription bubble by bending the DNA. This bending facilitates the breaking of the relatively weak bonds between the Ts and As that are prevalent in the TBP's binding sequence (TATA box).

 

What are the many roles of Polymerase II C-terminal domain phosphorlyation?

 

What is unique about transcription in Eukaryotes?

In Eukaryotes, as opposed to Prokaryotes, transcription is not coupled to translation, although it is coupled to RNA processing (also new). Not only is there a 5' cap added to the newly made mRNA, but there is a polyA tail added afterward. Addtionally, the mRNA is not the final step before translation-the introns have to be spliced out of the pre mRNA, making the final, mature mRNA.

 

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Topic 15 Eukaryotic Transcriptional Regulation I

 

Important Vocabulary:

 

Activators: Activators bind and stabilize polymerase. They are less structured and "Sticky" to be able to hold on to DNA. Jobs of activators

     include: recruiting Pol II, recruiting general transcription factors, and stabilization.

 

 

HATs:  Histone Acetyl-transferases.  They are a family of proteins that catalyze the formation of an amide bond between the epsilon-amino group of an amino-terminal lysine residue of one of the core histone proteins (H2A, H2B, H3 and H4).  These are activators that increase acetylation, increase DNA availability, and increase transcription.

 

 

Important Concepts:

 

How do activators function in Eukaryotes?  Are there differences when compared to Prokaryotic activators?

How do we know that DNA binding and activation are separable components of Activators?

 

What problems do nucleosomes cause for transcription?

Nucleosomes cause problems for transcription because they have DNA tightly wrapped around their protein core.  The nucleosome has a "+" charge which holds onto the "-" charged DNA backbone.  This attraction between the two creates a very tight hold on the DNA which prevents polymerase from transcribing the DNA.  In order for this problem to be solved, the polymerase displaces the DNA from the nucleosome and forms a closed loop.  This occurs when the HATs cause acetylation of the histone therefore makes the "+" charge weaker and loosens nucleosomes hold on the DNA.  This loop causes torsion on the DNA and causes it to supercoil.  This allows the nucleosome to keep contact with the DNA behind the RNA polymerase which allows the RNA polymerase to transcribe the DNA without interference.

 

How do histone tail modifications, particularly acetylation, change chromatin structure?

What are the functions of Histone Acetylases and Deacetylases?

How do Repressors work?

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Topic 16 Eukaryotic Transcriptional Regulation II

 

Important Vocabulary:

 

Prader-Willi Syndrome- An inherited developmental disorder caused by a eukaryotic imprinting error. Symptoms include but are not limited to hypogonadism, almond shaped eyes, thin upper lip, rapid weight gain within the first six years, and feeding problems.

 

 

Important Concepts:

 

What is the difference between Euchromatin and Heterochromatin?

Euchromatin areas are places in DNA where genes are being actively transcribed.  They are less dense areas of chromatin because the histone tails have had acetyl groups added onto them. 

     Heterochromatin is characterized by a complete repression of transcription.  These densely packed areas of chromatin are usually found around centromeres, telomeres, and silent genes. 

What kind of Modifications of Histones and DNA are associated with active vs. silent chromatin?

What is imprinting and how does it work?

How does methylation ensure the inheritance of gene activation states?

Why would you want to reprogram the chromatin organization of a cell?

 

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Topic 17 RNA Structure, Ribozymes, and Regulatory RNA

 

Important Vocabulary:

 

Ribozyme- These are the enzymes that catalyze chemical reactions associated with RNA. The discovery of riboenzymes was innovative becuase it was originally thought that only proteins catalyzed reactions. A key example is the Hammerhead Riboenzyme. The Hammerhead Ribozyme is a structure with three stems. RNA cleaves itself when it folds into this shape.

 

Important Concepts:

 

What makes RNA different than DNA?

RNA is different than DNA in several ways. The main primary difference is that RNA is single stranded in nature while DNA is double stranded. The nitrogenous base Uracil is commonly found in RNA (instead of Thymine). RNA utilizes a ribose ring sugar featuring a 2' OH group (which enables many of the chemical reactions RNA undergoes). In contrast, DNA utilizes a deoxyribose sugar. Also, RNA features 5' --> 3' polarity.

 

What are the unique folding properties of single stranded RNA?

RNA has the power to fold in a very specialized fashion. For example, RNA bends to form hairpin loops to terminate transcription. RNA also has the ability to undergo Non-Watson Crick Pairing which could allow typically non-pairing bases such as G-U to pair together. Triple base pairing is also possible (U-A-U). 

 

What is mechanism by which RNA undergoes alkali hydrolysis?

What are Ribozymes and how do they work?

What is the difference between miRNA and siRNA?

Where are miRNAs coded for?

Why are miRNAs generally about 20-21 nucleotides long?

Why can the RNases Drosha and Dicer process all miRNAs?

How does RISC function?

 

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Topic 18 RNA Splicing

 

Important Vocabulary:

 

snRNPs- small nuclear ribonucleoproteins. A complex made of both snRNA (small nuclear RNA) and protein.  The snRNA works as the spliceosome, while the protein facilitates the function of the snRNA.

 

Important Concepts:

What is splicing?

What sequences are required for the splicing of introns?

What is the function of U1 and U2 snRNPs?  How is base pairing important for their function?

How are self-splicing introns related to the spliceosome?

What is alternative splicing?

How do Splicing repressors and Activators work?

How can Northern blots, RT-PCR, and In Situ Hybridization be used to learn about a particular gene’s mRNA and expression pattern?