Chapter 6*

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Author:
mse263
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107750
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Chapter 6*
Updated:
2011-10-10 13:08:13
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MCBI
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Exam 1
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  1. isoforms
    the various proteins encoded by alternatively spliced mRNAs expressed from one gene
  2. noncoding DNA constitutes ____% of human chromosomal DNA
    98.5%
  3. transposable (mobile) DNA elements
    sequences that can copy themselves and move throughout the genome
  4. chromatin
    complex of DNA and the proteins that organize it; can be visualized as individual chromosomes during mitosis
  5. enhancers
    transcriptional control regions; in eukaryotes, can be 50 bases or more away from exon coding regions
  6. types of RNA that don't encode proteins:
    • 1) tRNA
    • 2) rRNA
    • 3) microRNA (regulate mRNA stability and translation)
  7. monocistronic
    each mRNA molecule encodes a single protein (what most eukaryotic genomes are); unlike bacterial genomes which are polycistronic, meaning a single mRNA includes a coding region for several proteins (that often function together in a biological process)
  8. cistrons
    protein coding regions
  9. simple transcription unit
    type of DNA transcript that yields a single type of mRNA (primary transcript) which goes on to be translated into a sinlge protein
  10. complex transcription unit
    primary RNA transcript can be processed in a variety of different ways, leading to the formation of mRNAs composed of different exons (made from teh same DNA template); common in multicellular organisms
  11. alternative splicing
    explands the number of proteins encoded in the genomes of higher level organisms
  12. gene family
    a set of duplicated genes that encode proteins with similar but not identical amino acid sequences; the then encoded/closely related homologous proteins are called a protein family
  13. pseudogenes
    nonfunctional gene sequences, aka lost protein coding ability or are otherwise not expressed in the cell
  14. skipped 6.2
  15. transposition
    the process by which these sequences are copied and inserted into a new site in the genome
  16. two types of mobile elements:
    • 1) those that transpose directly as DNA (transposons)
    • 2) those that transpose via an RNA intermediate transcribed from the mobile element by RNA polymerase then converted back to DNA via reverse transcriptase (retrotransposons)
  17. how are retrotransposons analogous to retroviruses?
    similar b/c retrotransposons make an RNA copy of themselves, introduce this new copy into another site in the genome (using reverse transcriptase) while also remaining at their original location; this is the same mechanism by which retroviruses spread; retroviruses can be thought of as retrotransposons that evolved genes encoding viral coats
  18. mobile elements in BACTERIA transpose mostly as:
    DNA; in contrast, most mobile elements in eukaryotes are retrotransposons
  19. general structure of a transposon:
    • 1) direct-repeat sequence: 5 - 11 b.p.'s, most outer ends of transposon, sequence dictates which target site the element will be inserted into
    • 2) inverted repeat: 50 b.p.'s, region flanking central protein-coding region; define the boundaries of transposon
    • 3) protein-coding region: encodes transposase (enzyme REQUIRED for transposition of the sequence to its new site)
  20. transposase performs 3 fuctions:
    • 1) precisely exises the transposon element in the donor DNA (blunt-end cuts)
    • 2) makes staggered cuts in target DNA
    • 3) ligates the 3' ends of the transposon to the 5' ends of the cut target DNA

    -transposition is completed by the host-cell's DNA polymerase and ligase first filling in the missing nucleotides at the 3' ends of the target DNA (creating the direct repeats) and then joining the free ends
  21. DNA transposition during the S phase of the cell cycle can increase the copies of transposons:
    -S phase of the cell cycle is when DNA synthesis occurs; if the donor DNA is in the region of the daughter cell that has already replicated and the target DNA is in a region that has yet to be replicated, then there is a net increase in transposon sequences in that daughter cell's DNA; one of 4 germ cells has an extra copy of the transposon
  22. retrotransposons can be divided into two main categories:
    those with and those WITHOUT long terminal repeats (LTRs)
  23. long terminal repeats (LTRs)
    ~250-600 b.p.; flank central protein coding region of retrotransposon, important for the incorporation of element into target site; leftward LTR functions as promoter and directs host RNA polymerase to initiate transcription (at the 5' nucleotide of the R sequence???)
  24. LTR retrotransposons
    constitute 8% of human DNA; difference between retrotransposons and retroviruses is that retrotransposons don't code for envelope protein so they can't bud from host cell; can still transpose to new DNA target sites
  25. most common type of mobile elements in mammals:
    retrotransposons lacking LTR's
  26. reverse transcription of an RNA genome yielding a double stranded DNA molecule takes place in the:
    cytosol; DNA is then transported into the nucleus via a complex involving INTEGRASE: an enzyme encoded by retrotransposon that integrates the double stranded DNA into its target site via a similar mechanism as that used by transcriptase (for DNA transposons)
  27. nonviral retrotranposons
    transposons that lack LTRs; form two classes in mammalian genome: LINEs and SINEs
  28. LINEs (long interspersed elements)
    about 6 kb.'s long; are three major families (L1, L2, L3) in human DNA and L1 is the only one that transposes in the contemporary genome; make ip 21% of total human DNA

    • composed of:
    • -short direct repeats
    • -contain 2 long open reading frames:
    • 1) ORF1: ~1 kb long, encodes RNA binding protein
    • 2) ORF2: ~4 kb long, encodes protein similar to reverse transcriptase and exhibits endonuclease activity
  29. SINEs (short interspersed elements)
    300 b.p.'s long;

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