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    BMOL20090 PC1 Revision Questions With Answers V2

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    Tadhg Ó Maoldhomhnaigh
    This document contains questions and answers about eukaryotic gene expression and RNA processing. It discusses the three eukaryotic RNA polymerases, transcription factors involved in transcription initiation by RNA polymerase II, promoter elements, RNA capping, polyadenylation, splicing, and differences between prokaryotic and eukaryotic translation. Red text provides the answers and blue text includes additional details about each topic.

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    BMOL20090 PC1 Revision Questions With Answers V2

    Uploaded by

    Tadhg Ó Maoldhomhnaigh
    102 views5 pages
    This document contains questions and answers about eukaryotic gene expression and RNA processing. It discusses the three eukaryotic RNA polymerases, transcription factors involved in transcription initiation by RNA polymerase II, promoter elements, RNA capping, polyadenylation, splicing, and differences between prokaryotic and eukaryotic translation. Red text provides the answers and blue text includes additional details about each topic.

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    This document contains questions and answers about eukaryotic gene expression and RNA processing. It discusses the three eukaryotic RNA polymerases, transcription factors involved in transcription initiation by RNA polymerase II, promoter elements, RNA capping, polyadenylation, splicing, and differences between prokaryotic and eukaryotic translation. Red text provides the answers and blue text includes additional details about each topic.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    102 views5 pages

    BMOL20090 PC1 Revision Questions With Answers V2

    Uploaded by

    Tadhg Ó Maoldhomhnaigh
    This document contains questions and answers about eukaryotic gene expression and RNA processing. It discusses the three eukaryotic RNA polymerases, transcription factors involved in transcription initiation by RNA polymerase II, promoter elements, RNA capping, polyadenylation, splicing, and differences between prokaryotic and eukaryotic translation. Red text provides the answers and blue text includes additional details about each topic.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    of 5

    BMOL20090 PC1 Revision questions

    Red = The answer


    Blue = Extra details

    Q1. What are the functions of the three eukaryotic RNA polymerases?
    A1. RNA polymerase I transcribes rRNA, RNA polymerase II transcribes mRNA, RNA polymerase III
    transcribes tRNA.

    There are a few complications: some small nuclear snRNAs (that function in splicing) are transcribed by
    RNA polymerase II, some by RNA polymerase III. RNA polymerase III also transcribes an extra ribosomal
    RNA called 5.8S rRNA, this appears in the large ribosomal subunit.

    Q2. What is unusual about the carboxy-terminal domain (CTD) of the largest RNA polymerase II
    subunit?
    A2. It contains multiple repeats of a seven-residue AA sequence, which includes SER, THR and TYR
    residues.
    N. B. All polypeptides have a carboxy-terminus, in this module the term “CTD” refers to the carboxy-
    terminal domain of the largest RNA polymerase II polypeptide.

    Q3. What are the key components of a core promoter for RNA polymerase II?
    A3. A TATA box and an initiator; a few have just an initiator and a downstream positioning element
    (DPE).

    Q4. What are the basal transcription factors that enable RNA pol II to initiate?
    A4. TFIID, TFIIA, TFIIB, TFIIF, TFIIE and TFIIH. (D, A, B, Pol II + F, E, and H).

    Q5. What do all these transcription factors do?


    A5. TFIID includes TBP, this “finds” the promoter. TFIIA and TFIIB bind next and call in the RNA
    polymerase II (complexed with TFIIF, a stabilising protein)
    TFIIE and TFIIH have helicase and kinase subunits. The helicases unwind duplex DNA around the start
    point, the kinase phosphorylates the CTD. This releases the RNA polymerase from the initiation
    complex so it can migrate along the template and make the RNA transcript.

    Q6. What is an upstream element?


    1
    A6. A short sequence within a promoter that binds a transcriptional activator protein. Activator
    proteins make contact with basal transcription proteins (such as TFIID, A or B) and make initiation more
    efficient.

    Q7. What is a response element?


    A7. Basically, the same as an upstream element EXCEPT that the activator protein only binds when it is
    switched on by an external signal. An example of an external signal is an anabolic steroid, which
    increases transcription of muscle protein genes.

    Q8. What is an enhancer?


    A8. A 100 to 200 bp stretch of DNA that is densely packed with upstream elements and response
    elements.
    An enhancer significantly increases transcription from its promoter.
    An enhancer can be located many kb away from the promoter it influences, upstream or downstream.

    Q9. What is the cap structure?


    A9. A guanosine nucleotide attached to the 5’ end of the RNA. The guanine base is methylated and the
    linkage is 5’ to 5’.

    Q10. Which classes of RNA are capped?


    A10. The capping enzyme associates with RNA polymerase II so mRNAs are capped but rRNAs and
    tRNAs are not. Some small nuclear RNAs are transcribed by RNA polymerase II, these are also capped.

    Q11. What are the functions of the cap?


    A11. It protects the 5’ end of the mRNA from degradation. It also binds the small ribosomal subunit
    during transcription initiation.

    Q12. How are the 3’ ends of pre-mRNAs modified?


    A12. With a polyA tail. A specific protein binds to the sequence 5’ AAUAAA 3’ in the growing transcript,
    an endonuclease cleaves between 11 and 30 nucleotides downstream, then polyA polymerase adds up
    two 200 adenosine residues.

    Q13. What is the function of the polyA tail?


    A13. The tail protects the 3’ end. It also functions in circularising the “mRNA” or non-covalent binding
    of the 3’ end to the 5’ end. [Poly A binding protein interacts with eIF-4G, which in turn interacts with
    2
    eIF-4E bound to the cap]. This probably makes repeated rounds of translation more efficient, and
    extends the longevity of mRNAs. These have to be stable because they are transported out of the
    nucleus for translation.

    Q14. What are the characteristics of an intron?


    A14. Introns start with GU and end with AG. There are poorly conserved consensus sequences at each
    end that include these dinucleotides. Introns have another poorly conserved element that includes the
    branch point adenosine.
    The distance between the 5’ end of the intron and the branch point can be anything between 50 and
    50,000 nucleotides.
    The distance between the branch point and the 3’ end is usually between 18 and 40 nucleotides.

    Q15. How would you describe the key steps in the splicing process (as concisely as possible)? Be as
    concise as possible.
    A15. See diagram below. The 2’ hydroxyl of the branch point A splits the exon 1-intron junction. This
    releases exon 1 (the upstream exon). In this first step, the 2’ carbon of the branch point ribose
    becomes linked to the 5’ end of the intron to form a lariat or loop. In the second step, the exposed 3’
    OH of exon 1 attacks the intron-exon 2 junction, this results in precise joining of the two exons and
    release of the intron as a lariat.

    3
    Q16. How does the spliceosome catalyse splicing, and how are exactly the right phosphodiester bonds
    broken and formed?
    A16. The U1 snRNA identifies the GU consensus at the 5’ end of the intron by base-pairing with it.
    The U2 snRNA identifies the branch point sequence by base-pairing, except that the branch point A is
    bulged out from an imperfect RNA double helix.
    The U1 and U2 snRNAs interact, this brings the branch point A close to the exon-intron junction.
    The U4-U5-U6 snRNAs join the complex. U2 and U6 form an active site that catalyses the two steps in
    the reaction.

    4
    The spliceosome RNAs form an active site similar to that of a protein enzyme; this lowers activation
    energies for the two reactions that make and break phosphodiester bonds. Also specific nucleobases in
    the snRNAs act as general acids and bases (for example, during the initial deprotonation of the 2’
    hydroxyl of the branch point, also protonation of the 3’ OH of exon 1 as the junction is cleaved etc)].

    Q17. How is eukaryotic translation different from prokaryotic translation?

    A17. In prokaryotes a RBS precedes the start codon in mRNA. The RBS has a sequence AGGAG, this
    base-pairs with a stretch of 16S rRNA in the small ribosomal subunit. This is important in translation
    initiation.
    In eukaryotes, a protein called eIFE4 (eukaryotic initiation factor E4) binds to the 5’ cap. This then binds
    a complex of the small 18S ribosomal subunit and methionyl-tRNA. The ribosomal subunit migrates
    along the mRNA until it reaches the first AUG start codon. Then the large ribosomal subunit joins and
    translation starts.

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