ch21 rna

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ch21 rna
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2013-12-07 18:15:52
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  1. What is the central dogma of molecular biology?
    –Transcription

    –Translation
  2. What is the definition of “gene?”
    a unit of heredity that is transferred from a parent to offspring and is held to determine some characteristic of the offspring.
  3. Understand slide 3 showing differential gene
    expression



    • Gene A is transcribed
    • and translated much more efficiently than gene B.

    • •Efficiency of expression
    • can be regulated

    • –1
    • gene = many RNA copies

    • –1 RNA
    • = many protein copies
  4. Compare and contrast the structure and function of DNA and RNA.
    • •RNA
    • –Ribonucleotides
    • –U instead of T (also bp with A)
    • –Same phosphodiester linkages
    • –Mostly single-stranded
    • –Folds up into a variety of
    • structures
    • –Have structural and catalytic
    • functions
  5. Know what are meant by template, noncoding, coding, sense, and antisense strand.
    • After transcription,
    • the newly synthesized RNA is complementary to the template strand of DNA.
    • The nontemplate strand is also
    • called the coding strand.
  6. Know the general mechanism of transcription including what occurs in each of the
    four stages of transcription?
  7. In what ways is transcription different from DNA replication?
    • Four stages of
    • transcription
    • Only transcription
    • units are transcribed
    • Only 1 strand of DNA
    • is the template
    • Unidirectional
    • •Signals
    • encoded in DNA tell RNA polymerases where to start and stop.

    • The direction of transcription is determined by the orientation of the promoter and varies from gene to gene.
    • -Some genes are transcribed using one DNA strand as a template, whereas others are transcribed using the other DNA strand as
    • template.

  8. What is a promoter?
    • –Start signal for transcription
    • –Conserved sequences
    • –Described in the 5’ → 3’
    • direction on the coding strand (aka sense strand)
    • •RNA transcript is complementary
    • to template strand
    • •Template strand is noncoding, and is also called antisense
    • strand
    • –Asymmetrical: binds polymerase in
    • only one orientation
  9. How is the direction of transcription determined?


    • First transcribed
    • nucleotide is +1 (Startpoint) ; then goes +2, +3,
    • etc. in the 5’ → 3’ direction (“downstream’).

    • -1, -2, -3, etc. in
    • the 3’ → 5’ direction is “upstream”.
    • In E. coli, the main
    • functional promoter elements are usually centered around positions -10 and -35 (consensus sequences
    • shown above).
  10. If the direction of transcription is given, be able to tell which strand of DNA is
    the template.
    Moves along the DNA template 3’à 5’ and synthesizes RNA 5’ à 3’ using ribonucleoside triphosphates
  11. What is Startpoint +1? What does upstream or
    downstream mean?
    • First transcribed
    • nucleotide is +1 (Startpoint) ; then goes +2, +3,
    • etc. in the 5’ → 3’ direction (“downstream’). 

    • -1, -2, -3, etc. in
    • the 3’ → 5’ direction is “upstream”.
  12. Where is the main functional promoter sequences found in E. coli?
    • In E. coli, the main
    • functional promoter elements are usually centered around positions -10 and -35 (consensus sequences
    • shown above).
  13. What are the characteristics and functions of a RNA polymerase? In what ways is it
    different from a DNA polymerase?
    •RNA polymerase

    –Binds to promoter

    –Unwinds ds DNA

    –Does not need a primer

    –Moves along the DNA template 3’à 5’ and synthesizes RNA 5’ à 3’ using ribonucleoside triphosphates

    • –Proofreads but has a higher error
    • rate than DNA polymerase
  14. How does RNA polymerase know when to start or stop transcription?
    When it recognizes its promoter.

    • •Termination of transcription in bacterial
    • genes

    • –Occurs when RNA polymerase copies a sequence
    • called the termination signal

    • –After termination, RNA polymerase
    • can then bind σ factor again and reinitiate transcription at a promoter.
  15. What is a sigma factor and what is its role intranscription?
    •Bacteria

    • –Single RNA polymerase complex
    • with exchangeable s factors.

    •Sigma (s) factor, a subunit of RNA polymerase, recognizes promoter

    • •Once transcription has initiated,
    • s factor detaches

    • •Different s factors are specific for
    • different promoters.
  16. Are sigma factors found in eukaryotes?
    NO
  17. Explain the electron micrograph shown in slide 15. Which part of the “Christmas tree”
    represents the 5’ end of the gene, the 3’ end of the gene, the RNA polymerase,
    and the 5’ and 3’ ends of the nascent (newly synthesized) RNA transcripts? What
    is represented by the segment between the two “Christmas trees?”
    • Several RNA
    • polymerases can transcribe the same gene at the same time

    • Electron micrograph
    • showing many molecules of RNA pol. simultaneously transcribing each of two
    • adjacent rRNA genes.
  18. How many nuclear RNA polymerases are there in eukaryotes? Which one
    transcribes pre-mRNA? Which one transcribes pre-tRNA? Which one transcribes
    most of the pre-rRNA?
    •Eukaryotes

    • –Three nuclear RNA polymerase
    • complexes with some shared components, each complex is specialized in the
    • synthesis of different types of RNA

    • –Many different types of
    • promoters. Some are located downstream from +1. 


  19. What are core promoters as opposed to control elements?
    • Core promoters are only capable of
    • driving a basal (low) level of
    • transcription



    • Most protein-coding
    • genes have additional short sequences upstream or downstream (control elements) that improve the
    • promoter’s efficiency.
  20. Where are the core promoter sequences for RNA polymerase II relative to the
    Startpoint?
    DPE (downstream promoter element)

  21. What is the TATA box and where is it relative to the Startpoint?
    • The first part of the promoter that has the core TATA. TFIID has a subunit, called TBP or
    • TATA-binding protein. It is located -25 to -32 from the start point
  22. What are general or regulatory transcription factors and what are
    their roles in transcription? Are they found in prokaryotes?
    • •RNA polymerases in eukaryotes
    • require additional proteins called transcription
    • factors, some of which must bind before the RNA polymerase can bind

    • –Transcription factors interact
    • with each other, thus protein-protein interactions play a crucial role in the
    • binding stage of euk. transcription



    • –General transcription factors are proteins that are always
    • required

    • –There are also regulatory transcription factors to control expression of
    • particular genes

    Not found in prokaryotes
  23. What is special about the transcription factor TFIID?
    It is the first transcription factor that joins before others are attached to it. Then RNA polymerase joins.
  24. What is TBP?
    TATA-binding protein.
  25. What is a preinitiation complex?
  26. What are primary transcripts as opposed to
    mature RNA?
    • –Primary transcripts (pre-RNA)
    • undergo some chemical changes to become mature RNA
  27. What are primary transcripts also called?
    pre-RNA
  28. What is the most stable and abundant form of RNA in the cell?
    rRNA : most stable and abundant form of RNA in cells
  29. Know that each ribosome contains 3 (bacterial) or 4 (eukaryotic) rRNA molecules.
    Bacterial ribosomes are 70S and the eukaryotic ribosomes are 80S. S value is a
    measure of the velocity at which a particle sediments upon centrifugation.
  30. Know that there are four types of rRNA molecules in eukaryotes. Three of them were
    made from one transcription unit that are then cleaved to give rise to three
    mature rRNA molecules. The 4th rRNA was made from a separate
    transcription unit. Prokaryotes have only three types rRNA molecules, all made
    from the same transcription unit.
  31. Know that primary tRNA transcripts are also processed in eukaryotes. One of the
    processing involves the creation of unusual bases.
  32. Describe the secondary structure of a mature tRNA molecule.
  33. Are mRNA processed in E. coli?
    no
  34. In what three ways can eukaryotic mRNA be processed or modified? Where in the cell
    do these processes take place?
    • •Pre-mRNA processing
    • –Is coupled to transcription in
    • eukaryotes
    • •Need to transport mRNA out of
    • nucleus before eukaryotic translation can begin
  35. What functions are believed to be served by the 5’ and 3’ processing of mRNA?
    –5’ capping with 7-methylguanosine

    –3’ cleavage and polyadenylation (poly-A tail)

    •   (both 5’ and 3’ processing are
    • believed to stabilize mRNA and aid its export to cytoplasm and recognition by ribosomes)

    –Splicing: removal of introns
  36. Why can transcription and translation occur simultaneously in bacteria but not in
    eukaryotes?
    Bacterial rna do not need anymore processing becaise they dont have introns.
  37. What are spliceosomes, snRNAs, snRNPs, and splice sites?
    •Splicing of pre-mRNA: removal of introns

    –Performed by spliceosome (snRNPs + snRNAs)

    • •Introns are marked with conserved
    • sequences at their “5’ and 3’ splice sites”.

    • •snRNAs in the snRNPs (small nuclear ribonucleoproteins) recognize splice sites and
    • cleave RNA at the intron-exon borders and link exons

    • The snRNAs are thought to be the catalytic
    • components of the spliceosome. Catalytic RNAs are called “ribozymes.” 

    splice sites are the edges of the introns.
  38. What are the functions of snRNAs and why is it an example of “ribozymes”?
    • •The snRNAs are thought to be the catalytic
    • components of the spliceosome. Catalytic RNAs are called “ribozymes.”
  39. know that 5’ and 3’ splice sites are recognized for precise splicing, a lariat
    structure is formed during splicing, and that excised introns are typically
    (there are exceptions as some types of snoRNAs are derived from introns)
    degraded.
  40. What are exons and introns?
    introns are junk DNA and exons are part of DNA that carry genes.
  41. What does alternative splicing mean?
    • •Alternative splicing can generate different
    • mRNAs from one primary transcript

    –1 Pre-mRNA à different versions of mature mRNA

    • •More than half of all human genes are
    • alternatively processed to give rise to two or more products.
  42. What are some different ways to alternatively
    splice?
  43. What’s the advantage of having alternative splicing?
    Allows genetic inovation. Different versions of mRNA can be used by different cells.
  44. Relatively speaking, do most mRNA molecules have long or short life span?
    • •Most mRNA molecules have a high turnover rate
    • (or short half-life)

    • –Turnover is measured in terms of
    • a molecule’s half-life, the length of time required for 50% of the molecules to
    • degrade

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