The Structure of Eukaryotic Chromatin

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The Structure of Eukaryotic Chromatin

• Compare the structure and organization of
  prokaryotic and eukaryotic genomes
• Describe the current model for progressive levels
  of DNA packing in eukaryotes
• Explain how histones influence folding in
  eukaryotic DNA
• Distinguish between heterochromatin and
  euchromatin.   

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The Control of Gene Expression

• Explain the relationship between differentiation
  and differential gene expression
• Describe at what level gene expression is
  generally controlled
• Explain how DNA methylation and histone
  acetylation affect chromatin structure and the
  regulation of transcription
• Define epigenetic inheritance
• Describe the processing of pre-mRNA in eukaryotes
• Define control elements and explain how they
  influence transcription
• Distinguish between general and specific
  transcription factors
• Explain the role that promoters, enhancers,
  activators, and repressors may play in
  transcriptional control
• Explain how eukaryotic genes can be coordinately
  expressed and give some examples of coordinate
  gene expression in eukaryotes
• Describe the process and significance of
  alternative RNA splicing

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The Molecular Biology of Cancer

• Distinguish between proto-oncogenes and
  oncogenes. Describe three genetic changes that
  can convert proto-oncogenes into oncogenes
• Explain how mutations in tumor-suppressor genes
  can contribute to cancer
• Explain how excessive cell division can result
  from mutations in the ras proto-oncogenes
• Explain why a mutation knocking out the p53 gene
  can lead to excessive cell growth and cancer.
  Describe three ways that p53 prevents a cell from
  passing on mutations caused by DNA damage
• Describe the set of genetic factors typically
  associated with the development of cancer
• Explain how viruses can cause cancer. Describe
  several examples
• Explain how inherited cancer alleles can lead to
  a predisposition to certain cancers.   

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Genome Organization at the DNA Level

• Describe the structure and functions of the
  portions of eukaryotic DNA that do not encode
  protein or RNA
• Distinguish between transposons and
  retrotransposons
• Describe the structure and location of Alu
  elements in primate genomes
• Describe the structure and possible function of
  simple sequence DNA
• Using the genes for rRNA as an example, explain
  how multigene families of identical genes can be
  advantageous for a cell
• Using a-globin and b-globin genes as examples,
  describe how multigene families of nonidentical
  genes may have evolved
• Define pseudogenes. Explain how such genes may
  have evolved
• Describe the hypothesis for the evolution of
  a-lactalbumin from an ancestral lysozyme gene
• Explain how exon shuffling could lead to the
  formation of new proteins with novel functions
• Describe how transposition of an Alu element may
  allow the formation of new genetic combinations
  while retaining gene function.

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CHAPTER 18GENOME EXPRESSION IN EUKARYOTES
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Cell Differentiation

• Divergence in structure and function of
  different cell types as they become specialized
  in an organisms development
• Specialized cells (nerve, muscle) express only a
  small percentage of their genes. Transcription of
  enzymes must locate genes at right time

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• Developmental fate of embryonic cells determined
  by cytoplasmic content and cell position in
  embryo
• Chemical signals activate transcription factors
  which result in gene expression for other
  regulatory proteins

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Genome Arrangement

• Prokaryotic DNA
• Usually contain circular DNA (plasmid)
• Much smaller than eukaryotic DNA small nucleoid
  region visible with electron microscope
• Associated with few protein molecules
• Less elaborately structured and folded than
  eukaryotic. Loops anchored to plasma membrane

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Eukaryotic DNA

• Complex with large amount of protein to form
  chromatin
• Highly extended and tangled during interphase
• Condensed into short, thick, discrete chromosomes
  during mitosis when stained it is visible with a
  light microscope

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Nucleosomes

• Histones Small proteins rich in positive amino
  acids (arginine, lysine) that bind to negatively
  charged DNA forming chromatin

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• Nucleosome Basic unit of DNA packing formed
  from DNA wound around a protein core
• May control gene expression by controlling access
  of transcription proteins to DNA

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Looped domains

• Attached to non-histone protein scaffold
• Contain 20,000-100,000 base pairs
• Coil and fold, compacting chromatin into a
  mitotic chromosome
• Also exist in interphase

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• Heterochromatin Remains highly condensed during
  interphase not actively transcribed (ex. Barr
  bodies)
• Euchromatin Less condensed during interphase
  and is actively transcribed, but condenses during
  mitosis

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Genome Organization

• Repetitive Sequences
• Satellite DNA Highly repetitive DNA consisting
  of short unusual nucleotide sequences that are
  tandemly repeated thousands of times. Mostly
  located at tips centromere.
• Telomere Series of short tandem repeats at ends
  of chromosomes maintain integrity of lagging DNA
  strand during replication

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• Multigene Family (Fig. 18-3) Collection of
  genes that are similar or identical on sequence
  and of common ancestral origin may be clustered
  or dispersed in genome

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Control of Gene Expression
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Eukaryotic Gene Organization (Fig. 18.5)
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Transcriptional Control (Fig. 18.6)

• Gene transcription factors Proteins that must
  assemble on DNA at promoter (TATA box) before
  transcription can begin
• Gene regulatory proteins influence rate of
  transcription by speeding up or slowing down
  assembly process at promoter
• Enhancer Sequence Noncoding DNA control
  sequence to which transcription factors (gene
  regulatory proteins) bind, controlling
  transcription of structural genes may be distant
  from promoter
• Transcription factors have DNA binding sites
  called domains containing alpha helices and beta
  sheets

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Posttranscriptional Control Gene expression may
be stopped or enhanced at any of the following
steps

• RNA processing and export
• 5 cap and poly-A tail are added
• Introns removed and exons spliced together

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• Regulation of mRNA degradation
• Prokaryotic mRNA short lived
• Eukaryotic lifespan hours to weeks
• Longevity of mRNA affects how much protein
  synthesis is directs

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Translational/Posttranslational Control

• Binding of translation repressor protein to 5
  end can prevent ribosomal attachment
• Translation of all mRNAs can be blocked by
  inactivation of initiation factors (early
  embryonic development)
• Many polypeptides must be modified or transported
  before becoming active cleavage, addition of
  chemical groups

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Chromosomal Puffs Loops of decondensed DNA
appearing on polytene chromosomes where intense
transcription occurs

• Ecdysome (molting hormone) can induce changes
  in puff patterns

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Steroid Hormones (Fig 18.8) Chemical signals
that can activate gene expression in target cells
of vertebrates

• Lipid soluble Diffuse across plasma membrane
• Steroid enters nucleus, where it binds to
  steroid-receptor protein a DNA binding proteins
  that can activate transcription of a gene
• In absence of steroid, an inhibitory protein
  binds to the steroid receptor and blocks its DNA
  binding domain, preventing receptor from
  binding to DNA
• When a steroid is present, its binding to
  receptor causes release of inhibitory protein and
  activates the steroid receptor, so it can attach
  to DNA at enhancer sequences that control
  steroid-responsive gene

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Genome Alteration

• Gene Amplification Selective synthesis of DNA,
  which results in multiple copies of a single gene
• Amphibian rRNA genes amplified in oocyte to make
  large numbers of ribosomes needed to make
  proteins upon fertilization
• Occurs in cancer cells when exposed to high
  concentration of chemotherapeutic drugs
  amplified genes confer drug resistance

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• Chromosome Diminution Elimination of whole
  chromosomes or parts of chromosomes from certain
  cells in early embryonic development

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Rearrangements in Genome May activate or
inactivate certain genes

• Transposons can rearrange DNA by inserting into
  the middle of a coding sequence of another gene
  prevent interrupted gene from functioning
  normally
• Inserting within a sequence that regulates
  transcription. The transposition may increase or
  decrease a proteins production
• Inserting its own gene just downstream from an
  active promoter that activates its transcription

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Immunoglobulins Antibodies produced by B
lymphocytes that specifically recognize and help
combat pathogens

• B lymphocytes are very specialized each
  differentiated cell an its descendants produce
  only one specific antibody
• Antibody specificity and diversity are properties
  that emerge from the unique organization of the
  antibody gene, which is formed by rearrangement
  of the genome during B cell development

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• DNA Methylation Addition of methyl groups
  (-CH3) to bases of DNA. Genes that are
  methylated are not expressed

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Cancer

• Definition Variety of disease in which cells
  escape from the normal controls of growth and
  division, and can result from mutations that
  alter normal gene expression in somatic cells
• Carcinogen Physical agents, such as X-rays and
  chemical agents that cause cancer by mutating DNA
• Oncogene Gene responsible for cell becoming
  cancerous

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Proto-oncogene Gene that normally codes for
regulatory proteins controlling cell growth,
division an adhesion, and that can be transformed
by mutations into an oncogene. Caused by 4 types
of mutations

• Gene amplification extra copies of oncogenes
• Chromosome translocation in a new position,
  oncogenes may be next to an active promoter or
  other control sequences that enhance
  transcription

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• Gene transposition Oncogene may move to a new
  locus near an active promoter, or a promoter may
  be moved upstream of an oncogene
• Point mutation A slight change in the
  nucleotide sequence might produce a growth
  stimulating protein that is more active or more
  resistant to degradation than the normal protein

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