1' Discuss the contributions of Mayer'

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1. Discuss the contributions of Mayer.

• Mayer demonstrated that the stunting disease of
  tobacco plants was contagious ? thought it was
  caused by an unusually small bacteria
• - later findings demonstrated that the disease
  could not be bacteria-caused, but must be a
  particle much smaller (and unlike) a bacterium
• - the infectious particle was finally
  crystallized and observed and is now known as the
  tobacco mosaic virus (TMV) ?

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2. List and describe the structural components of
viruses, and explain why viruses are obligate
parasites.

• It is a genome enclosed in a protective coat
• It is organized as single nucleic acid molecules
• May have 4 to several hundred genes
• Simple composition ?
• 1. Capsid protein coat that encloses the viral
  genome
• 2. Envelope membrane that cloaks some viral
  capsids (head, sheath, DNA, tail fibers)
• Viruses express their genes and reproduce only
  within a living cell ?

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3. Briefly describe what happens when a virus
infects a host cell.

• A viral infection begins when the genome of a
  virus makes its way into a host cell ?

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4. Distinguish between lytic and lysogenic
reproductive cycles using phage T4 and phage ? as
examples.

• Lytic Cycle
• Viral replication cycle that results in the death
  (or lysis) of the host cell
• T4 ? phage attaches to cell surface, phage
  contracts sheath and injects DNA, hydrolytic
  enzymes destroy the host cells DNA, phage genome
  directs the host cell to make phage components
  and cell lyses and releases phage particles

• Lysogenic Cycle
• A viral replication cycle that involves the
  incorporation of the viral genome into the host
  cell genome
• ? phage binds to the surface of ecoli and injects
  the DNA and inserts it by genetic recombination ?

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5. Using viruses with envelopes and RNA as
examples, describe variations in replication
cycles of animal viruses.

• Enveloped Viruses are characterized by
• Attachment
• Entry
• Uncoating
• Viral RNA protein synthesis
• Assembly and release

• RNA as viral genetic material
• RNA viruses can be complicated (like
  retroviruses)
• mRNA or the strand that corresponds to mRNA is
  the strand and it has the nucleotide sequence
  that codes for proteins
• The strand is a template for synthesis of the
  strand ?

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6. Describe what vaccines are and how they are
manufactured.

• Vaccine ? a harmless variant or derivative of
  pathogenic microbes that stimulate the immune
  system to mount defenses against the actual
  pathogen ?

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7. Explain the role of reverse transcriptase in
retroviruses.

• It is the enzyme that transcribes DNA from an RNA
  template
• Viral genomic RNA
• (reverse transcriptase)
• Viral DNA ?

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8. Describe how viruses recognize host cells.

• They recognize their host cell by a complementary
  fit between external viral proteins and specific
  cell surface receptor sites ?

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9. Describe several defenses bacteria have
against phage infection.

• Bacterial mutations can change receptor sites to
  avoid recognition
• - this in turn prevents infection
• Restriction nucleases in bacteria recognize and
  cut up foreign DNA
• - self-destruction is avoided because bacterial
  DNA is chemically altered ?

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10. Explain how viruses may cause disease
symptoms, and describe some medical weapons used
to fight viral infections.

• Viruses damage or kill cells (viral infection ?
  lysosome releases hydrolytic enzymes)
• They can be toxic or cause infected cells to
  produce toxins
• Cause varying degrees of cell damage
• Immune system reacts, causing fever, aches,
  inflammation
• Vaccines harmless variants or derivatives of
  pathogenic microbes that mobilize the immune
  system
• Antiviral drugs fight after the disease ?

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11. List some viruses that have been implicated
in human cancers, and explain how tumor viruses
transform cells.

• Retrovirus adult leukemia
• Herpes virus Epstein-Barr (mono) ? Burkitts
  lymphoma
• Papovavirus human warts cervical cancer
• Hepatitis B virus chronic hepatitis liver
  cancer
• Tumor viruses transform cells by inserting viral
  nucleic acids into host cell DNA
• - this insertion is permanent as the provirus
  never excises
• - insertion for DNA tumor viruses is
  straightforward ?

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12. Distinguish between horizontal and vertical
routes of viral transmission in plants.

• Horizontal ? route of viral infection in which an
  organism receives the virus from an external
  source
• Vertical ? route in which an organism inherits a
  viral infection from its parent ?

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13. List some characteristics that viruses share
with living organisms, and explain why viruses do
not fit our usual definition of life.

• CAN mutate and evolve
• - have a genome with the same genetic code as
  living organisms
• CANNOT reproduce independently
• Need a host cell for reproduction ?

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14. Provide evidence that viruses probably
evolved from fragments of cellular nucleic acid.

• Genetic material of different viral families is
  more similar to host genomes than to that of
  other viral families
• Some viral genes are identical to cellular genes
• Viruses of eukaryotes are more similar in genomic
  structure to their cellular hosts than to
  bacterial viruses
• Viral genomes are similar to cellular genetic
  elements like plasmids and transposons ?

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15. Describe the structure of a bacterial
chromosome.

• It is composed of one double stranded, circular
  molecule of DNA
• Structurally simpler and has fewer associated
  proteins than a eukaryotic chromosome
• Found in the nucleoid region of the cell ?

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16. Describe the process of binary fission in
bacteria, and explain why replication of the
bacterial chromosome is considered to be
semiconservative.

• Binary fission is preceded by DNA replication,
  which begins at a single origin on the chromosome
• It is an asexual process, producing clones
• 2 replication forks move bi-directionally until
  they meet and replication is complete
• Bacteria can divide every 20 minutes ?

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17. List and describe the three natural processes
of genetic recombination in bacteria.

• Transformation ? process of gene transfer during
  which a bacterial cell assimilates foreign DNA
  from the surroundings ?

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• 2. Transduction ? gene transfer from one
  bacterium to another by a bacteriophage
• 3. Conjugation ? the direct transfer of genes
  between two cells that are temporarily joined ?

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18. Distinguish between general transduction and
specialized transduction.

• Generalized ? transduction that occurs when
  random pieces of host cell DNA are packaged
  within a phage capsid during the lytic cycle of a
  phage
• Specialized ? occurs when a prophage excises from
  the bacterial chromosome and carries with it only
  certain host genes adjacent to the excision site
  (AKA restricted transduction) ?

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19. Explain how the F plasmid controls
conjugation in bacteria.

• The ability to form sex pili and to transfer DNA
  is conferred by genes in a plasmid called the F
  plasmid ?

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20. Explain how bacterial conjugation differs
from sexual reproduction in eukaryotic organisms.

• Conjugation ? transfer of genes only ( no
  offspring)
• Sexual reproduction ? donation of genetic
  material to an offspring ?

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21. For donor and recipient bacterial cells,
predict the consequences of conjugation between
the following 1) F and F- cell 2) Hfr and F-
cell

• 1. The F factor (which is in the F) replicates
  and one copy is tranferred to the F_
• Only some bacterial genes are donated
• The recipient F- cell does not become F because
  only part of the F factor transferred
• The recipient cell becomes a partial diploid
• 2. As the integrated F factor of the Hfr cell
  transfers to the F- cell, it pulls the bacterial
  chromosome behind its leading end ? the
  conjugation bridge usually breaks before the
  entire chromosome and tail end of the F factor
  can be transferred
• As a result
• Only some bacterial genes are donated
• Recombination occurs between the Hfr chromosomal
  fragment and the F- cell homologous strand
  exchange results in a recombinant F- cell ?

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22. Define transposon, and describe two essential
types of nucleotide sequences found in transposon
DNA.

• Transposons ? DNA sequences that can move from
  one chromosomal site to another
• Insertion sequences ? the simplest, they contain
  only the genes necessary for the process of
  transposition (2 essential types)
• - nucleotide sequence coding for transposase
  (which catalyzes insertion of transposons into
  new chromosomal sites)
• - inverted repeats ?

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23. Distinguish between an insertion sequence and
a composite transposon.

• Insertion ? the simplest transposons, they
  contain only the genes necessary for the process
  of transposition
• Composite ? transposons which include additional
  genetic material besides that required for
  transposition consist of one or more genes
  flanked by insertion sequences ?

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24. Briefly describe two main strategies cells
use to control metabolism.

• Regulation of enzyme activity ? the catalytic
  activity of many enzymes increases or decreases
  in response to chemical cues
• Regulation of gene expression ? enzyme
  concentrations may rise and fall in response to
  cellular metabolic changes that switch genes on
  or off ?

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25. Explain why grouping genes into an operon can
be advantageous.

• Operon ? a regulated cluster of adjacent
  structural genes (gene that codes for a
  polypeptide) with related functions
• - common in bacteria and phages ?

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26. Using the trp operon as an example, explain
the concept of an operon and the function of the
operator, repressor, and corepressor.

• Mechanism for the control of gene expression
• Operator ? a DNA segment located within the
  promoter or between the promoter and structural
  genes, which controls access of RNA polymerase to
  structural genes
• Repressor ? specific protein that binds to an
  operator and blocks transcription of the operon
• Corepressor ?a molecule, usually a metabolite,
  that binds to a repressor protein, causing the
  repressor to change into its active conformation ?

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27. Distinguish between structural and regulatory
genes.

• Structural genes ? gene that codes for a
  polypeptide
• Regulatory genes ? genes that code for repressor
  or regulators of other genes ?

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28. Describe how the lac operon functions and
explain the role of the inducer allolactose.

• Operon that can be switched on or induced
• Lactose metabolism in Ecoli is programmed by the
  lac operon with 3 structural genes
• 1. Lac Z codes for ß galactosidase which
  hydrolyzes lactose
• 2. Lac Y codes for permease which transports
  lactose into the cell
• 3. Lac A codes for transacetylase which has no
  known role
• Has a single promoter and operator
• Allolactose ? an isomer of lactose, acts as an
  inducer to turn on the lac operon ?

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29. Explain how repressible and inducible enzymes
differ and how these differences reflect
differences in the pathways they control.

• Repressible
• Genes are switched on until a specific metabolite
  activates the repressor
• Generally function in anabolic pathways
• Pathway end product switches off its own
  production by repressing enzyme synthesis

• Inducible
• Their genes are switched off until a specific
  metabolite inactivates the repressor
• Function in catabolic pathways
• Enzyme synthesis is switched on by the nutrient
  the path uses ?

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30. Distinguish between positive and negative
control, and give examples of each from the lac
operon.

• Negative
• Binding of active repressor to an operator always
  turns off structural gene expression
• Lac ? negative by repressor protein

• Positive
• Occurs only if an activator molecule interacts
  directly with the genome to turn on transcription
• Lac ? positive by cAMP receptor protein (CRP) ?

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31. Explain how cAMP is affected by glucose
concentration.

• When no glucose ? The cell accumulates cAMP, a
  nucleotide derived from ATP.
• - cAMP activates CRP so that it can bind to the
  lac promoter
• When glucose concentration increases, glucose
  catabolism decreases the intracellular
  concentration of cAMP
• - thus, cAMP releases CRP ?

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32. Describe how E. coli uses the negative and
positive controls of the lac operon to economize
on RNA and protein synthesis.

• CRP is an activator of several different operons
  that program catabolic pathways
• Glucoses presence deactivates CRP, which slows
  synthesis of those enzymes a cell needs to use
  catabolites other than glucose
• Ecoli prefers using glucose as its primary carbon
  and energy source and the enzymes for this are
  coded for by unregulated genes that are
  continuously transcribed ? the end