Microbio Final pt 3

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  1. DNA information is transcribed from the ______
    DNA information is transcribed from the anti-sense strand (3’ hydroxyl - 5’ phosphate)
  2. The _____strand of DNA is transcribed into a mRNA
    The anti-sense strand of DNA is transcribed into a mRNA
  3. The ______ is translated into the amino acid sequence of the polypeptide chain.
    The mRNA nucleotide sequence is translated into the amino acid sequence of the polypeptide chain.
  4. How is a gene described?
    A gene is defined as the nucleotide sequence coding for a single polypeptide chain, rRNA or tRNA.
  5. What type of mRNA do Prokaryotes have?
    Single mRNA that contains more than one coding region (or more than one gene). (Polycistronic)

    One RNA can code two or more proteins

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  6. What type of mRNA do Eukaryotes have (and how is it formed?)
    In Eukaryotes, the DNA contains introns and exons.

    The Primary RNA transcript must undergo processing which means the introns must be removed and the exons are spliced back together to make mature mRNA that is transported to the cytoplasm.

    The mRNAs of eukaryotes are almost always monocistronic (only coding for one polypeptide chain)

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  7. What is the eukaryotic splicesosome responsible for?
    It is responsible for the removal of introns and joining of adjacent exons to form a mature mRNA.
  8. Before splicing can occur in eukaryotes via the splicesosome, what must occur?
    • 1. Capping - Before transcription is complete, addition of a methylated guanine nucleotide at the 5’ phosphate end must occur
    • Purpose: Promotes formation of initiation complex between mRNA and ribosome (later)

    • 2. Trimming the 3’ end and adding a poly A tail (not translated & stabilizes mRNA). Must be removed before mRNA is degraded.
    • Purpose: Aids the mRNA's survival in the cytoplasm.

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  9. Describe the structure of DNA
    Polymer of deoxyribonucleotides held together by 3’-5’ phospho-diester bonds.

    DNA is double stranded and anti-parallel, with the two strands held together by hydrogen-bonding between nitrogenous bases

    Purines (two rings) bind to pyrimidines (one ring):

    • Adenine (purine) binds to Thymine (pyrimidine) w/ 2 hydrogen bonds
    • Guanine (purine) binds to Cytosine (pyrimidine) w/ 3 hydrogen bonds

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  10. Which bonds found in DNA are susceptible to breaking as temperature rises?
    The hydrogen bonds between the bases will break as temperature is raised, but not the covalent bonds.

    (Tm value: melting temperature)
  11. Contrast the DNA of Eukaryote with Prokaryotes
    The DNA in Eukaryotes associates with basic proteins called histones to form a nucleosome

    In Prokaryotes, the DNA is also double stranded but the ends are closed to make a circle (Closed circle, Nicked, Supercoiled)

    In both cases though, the DNA is highly coiled
  12. Describe the DNA (or RNA) of Viruses, Viroids, and Plasmids
    Viruses: contain DNA or RNA (Mimi virus has both!)

    Viroids: contain small pieces of RNA

    Plasmids: Contain small genetic elements that exist and replicate separately from the major bacterial “chromosome”. Most are circular polynucleotides that do not usually cause cell damage and they do not have extra cellular forms. (Some can integrate into host DNA.)
  13. DNA replication is what kind of process? Who proved this/how?
    DNA replication is semiconservative, as proved by Messelson and Stahl (know the experiment and how to predict generations).

    If DNA is labeled with heavy N15 Nitrogen and then the cells are allowed to replicate (1st generation) in light nitrogen, N14, the DNA in the daughter cells will be of a hybrid density.

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  14. DNA is unwinded by ______.
    DNA is unwinded by Helicase (dnaB)
  15. The energy for DNA Helicase to perform its action is provided by ______.
  16. Single strands of DNA are stabilized by ______.
    Single strands of DNA are stabilized by single stranded binding proteins (ssb)
  17. What does DNA polymerase require before it can begin replication?
    DNA polymerase can not replicate a strand de novo, because it requires a primer. Therefore a small RNA primer is synthesized by primase in the 5’ to 3’ direction & initiates DNA synthesis by DNA polymerase III.
  18. In what direction can DNA polymerase III synthesize new DNA?
    DNA polymerase III can only synthesize in the 5’ to 3’ direction, so it can do so continuously on the leading strand but must synthesize DNA in segments in the lagging strand.
  19. Lagging strand (segments) are called what? What must each have done to it?
    These segments are called Okazaki fragments & each must be separately primed, but in contrast, the leading strand is only primed once.

    DNA Polymerase III synthesizes in the 5’ to 3’ direction toward the RNA primer of a previously synthesized fragment on the lagging strand. Once DNA Polymerase III reaches the primer of the next fragment, DNA Polymerase I comes in and replaces III, it removes the primer and synthesizes DNA.

    Following the work of DNA polymerase I, DNA ligase comes in and links the 3’ hydroxyl to the 5’ phosphate on the lagging strand.
  20. Describe the process of sealing two fragments on the lagging strand.
    • (a) DNA polymerase III is synthesizing DNA in the 59 S 39 direction toward the RNA primer of a previously synthesized fragment on the lagging strand.
    • (b) On reaching the fragment, DNA polymerase III leaves and is replaced by DNA polymerase I.
    • (c) DNA polymerase I continues synthesizing DNA while removing the RNA primer from the previous fragment.
    • (d) DNA ligase replaces DNA polymerase I after the primer has been removed.
    • (e) DNA ligase seals the two fragments together.

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  21. DNA is transcribed into RNA by _____ via the process of _____.
    DNA is transcribed into RNA by RNA polymerase via the process of transcription 
  22. What is the basic structure of RNA polymerase?
    Structure: Consist of a sigma subunit and core enzyme.

    • Sigma → Recognizes promoter 
    • Core enzyme → Synthesizes RNA to termination site.
  23. For RNA synthesis to begin, what must RNA polymerase recognize first?
    RNA polymerase must recognize starting region (promoter) for synthesis to begin; this region is recognized by the sigma factor of RNA Polymerase.

    • Pribnow box → Promoter
    • -35 & -10
  24. What is the Pribnow box?
    The Pribnow box is the region of DNA to which RNA polymerase binds before initiating transcription of DNA into RNA.

    Most bacterial promoters contain two consensus sequences, -10 & -35.

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  25. Transcription–Chain Termination is caused by what?
    Inverted repeats (caused by hydrogen bonding together) in transcribed DNA form a stem-loop structure in RNA that terminates transcription.

    The stem-loop is upstream from a run of uracils.

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  26. Describe the process of Translation/Codon-Anticodon recognition
    tRNA has an anticodon that pairs with the codon on mRNA to bring the correct amino acid to the site of the growing polypeptide chain (in the ribosome).

    Amino acids must be activated before binding to tRNA by reacting with ATP to form amino acyl-AMP, which then reacts with tRNA releasing AMP and adding the amino acid to the 3’ end of tRNA.

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  27. Good Graphic for Translation (Initiation+Elongation)
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  28. Mutations involving one base pair are called __________
    Mutations involving one base pair are called point mutations
  29. Point mutations result from _______. If it occurs in the coding region, ______ outcomes may result.
    Point mutations result from base pair substitutions, insertion, or deletion. If it occurs in the coding region, different outcomes may result.
  30. What different kinds of mutations can occur?
    Silent, Nonsense, or Missense mutations 

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  31. Virus Particle is called a _____
    Virus Particle is called a viron
  32. How can one quantify a viral population?
    Via the Plaque Count Assay

    Process: Top agar contains phage dilution and is seeded with bacterial host cells.  Where a single virion is present it replicates and lyses the host cell releasing many virions that infect cells  in the vicinity and undergo repeated lytic cycles eventually clearing the cells  forming a plaque
  33. In the replication of animal viruses, penetration involves what?
    Penetration involves entrance of both protein coat and nucleic acid (unlike bacterial viruses), an uncoating enzyme removes the protein coat following penetration.
  34. Describe the Hershey-Chase Experiment
    The Hershey-Chase experiment with bacteriophages supported DNA as genetic material.

    They labeled DNA with P32 (phosphorus label) and the protein with S35 (sulfur label) and observed that the phosphorous label went into the host cell. Most of the sulfur stayed on the outside.

    But if they had used an animal virus, they would have both labels go in.
  35. What pathways may a Bacteriophage follow?
    Lytic: Virulent - (Virus replication occurs and host is lysed)

    Lysogenic: Nonvirulent - (Viral nucleic acid is integrated into host chromosome and replicates as the host DNA replicates). When integrated, viral DNA is called a prophage and can be induced to begin a lytic cycle.

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  36. What are the possible effects that an animal virus may have on host cell it infects?
    Latent infection – Present but not causing harm (may be induced to lytic infection). Chicken pox, latent in nerve cells, later emerges to cause shingles.

    Persistent – Slow release of virus without cell death

    Virulent – Lytic (death and release of virions, lysis is not always occuring)

    Transformation – Causes tumors
  37. Describe the Retrovirus, and it's process of replication
    It is a single-stranded RNA virus that penetrates into animal cells and is uncoated.

    It has a reverse transcriptase enzyme that converts single-stranded RNA into a complementary DNA that is converted to double-stranded DNA.

    The dsDNA is integrated into host -DNA.

    When it is transcribed, it produces viral ssRNA and protein coat subunits that are assembled into the virion which is released by a budding process that places host membrane

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  38. What are the three mechanisms in which Bacteria may transfer genes?
    1) Transformation → Genetic transfer mediated by extracellular DNA.

    2) Transduction → Genetic transfer mediated by viruses.

    • Generalized: pieces of host DNA enclosed in a capsid infects another cell bringing new host genes.
    • Restricted: viral DNA is integrated into host DNA, when induced some bacterial genes are excised with some viral genes and transferred to the host.

    3) Conjugation → DNA transfer from donor to recipient cell mediated by cell to cell contact.

    • F+ → F- (Plasmid transferred while replicated) 
    • Hfr → F- (F-factor is integrated into major bacterial chromosome, so both plasmid and chromosome genes get transferred)

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  39. Describe the process of Transformation
    Transformation is a genetic transfer process by which free DNA is incorporated into a recipient cell and brings about genetic change.

    Transfer occurs by pieces of extracellular DNA when the donor lyses.

    • (a) Binding of double-stranded DNA by a membrane-bound DNA-binding protein
    • (b) Passage of one of the two strands into the cell while nuclease activity degrades the other strand
    • (c) The single strand in the cell is bound by specific proteins, and recombination with homologous regions of the bacterial chromosome is mediated by RecA protein
    • (d) Transformed cell.

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  40. Describe the Transduction process of bacterial genetics
    Transduction → Genetic transfer mediated by viruses.

    • Generalized: pieces of host DNA enclosed in a capsid infects another cell bringing new host genes.
    • Restricted: viral DNA is integrated into host DNA, when induced some bacterial genes are excised with some viral genes and transferred to the host.
  41. Describe the Restricted Transduction process of bacterial genetics
    Normal vs Incorrect excision

    • Normal → prophage loops out correctly and is excised releasing viral DNA
    • Incorrect → Integrated viral DNA excised incorrectly, a piece of host DNA is exchanged for viral DNA. It detaches and replicates viruses with both viral and host DNA that transfer genes to another host
  42. Describe the Conjugation process of bacterial genetics
    F+ x FF:

    • plasmid is replicated as it is transferred.
    • F+ keeps a copy, F+ stays F+
    • F- becomes F+


    • Plasmid is integrated in Hfr as part of the bacterial DNA.
    • A break occurs in one strand in the middle of plasmid genes and transfer occurs including both the plasmid and major chromosome genes.
    • Break occurs before complete transfer thus F- stays F-.

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  43. Three types of RNA take place in protein synthesis; what are they, and what does each do?
    Messenger RNA (mRNA): is a single-stranded molecule that carries the genetic information from DNA to the ribosome, the protein-synthesizing machine.

    Transfer RNAs (tRNAs): convert the genetic information on mRNA into the language of proteins.

    Ribosomal RNAs (rRNAs): are important catalytic and structural components of the ribosome.
  44. The molecular processes of genetic information flow can be divided into three stages; describe each
    1. Replication: During replication, the DNA double helix is dupli- cated, producing two double helices.

    2. Transcription: Transfer of information from DNA to RNA is called transcription.

    3.Translation: Synthesis of a protein, using the information carried by mRNA, is known as translation.
  45. What does it mean that DNA replication is semiconservative?
    Replication is semiconservative, meaning that the two resulting double helices consist of one new strand and one parental strand
  46. What is the fate of transferred bacterial DNA?
    Whether it is transferred by transformation, transduction, or conjugation, the incoming DNA faces three possible fates:

    (1) It may be degraded by restriction enzymes;

    (2) it may replicate by itself (but only if it possesses its own origin of replication such as a plasmid or phage genome)

    (3) it may recombine with the host chromosome.
Card Set
Microbio Final pt 3
Microbio Final pt 3
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