Eukaryotic Genomes

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Eukaryotic Genomes
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Eukaryotic Genomes

• In eukaryotes, the DNA-protein complex, called
  chromatin is ordered into higher structural
  levels than the DNA-protein complex in
  prokaryotes
• Chromatin structure is based on successive levels
  of DNA packing
• Eukaryotic DNA is precisely combined with a large
  amount of protein
• Eukaryotic chromosomes contain an enormous amount
  of DNA relative to their condensed length

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Nucleosomes Beads on a String

• Proteins called histones are responsible for the
  first level of DNA packing in chromatin
• Histones bind tightly to DNA and their
  association seems to remain intact throughout the
  cell cycle
• In electron micrographs unfolded chromatin has
  the appearance of beads on a string
• Each bead is a nucleosome - the basic unit of
  DNA packing

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Higher Levels of DNA Packing

• The next level of packing forms the 30-nm
  chromatin fiber
• The 30-nm fiber, in turn forms looped domains,
  making up a 300-nm fiber

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Chromatin Condensation

• In interphase cells most chromatin is in the
  highly extended form called euchromatin
• In a mitotic chromosome the looped domains
  themselves coil and fold forming the
  characteristic metaphase chromosome

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Eukaryotic Gene Regulation

• In eukaryotes, gene regulation is more complex
• Many key stages of gene expression can be
  regulated in eukaryotic cells
• However, transcriptional controls are still the
  primary method of gene regulation
• But there are also posttranscriptional controls.

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Eukaryotic Gene Regulation - Transcription

• Chromatin modification
• Histone modification
• DNA methylation
• Transcription factors and control Elements
• Activators
• Repressors

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Eukaryotic Gene Regulation - Transcripton

• Coiling of DNA within the nucleus help regulate
  gene transcription in eukaryotes.
• Studies have shown that transcription factors are
  unable to bind to promoters located in regions of
  DNA that are coiled around the histones of a
  nucleosome

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Chromatin Modification

• Chromatin-modifying enzymes provide initial
  control of gene expression
• By making a region of DNA either more or less
  able to bind the transcription machinery
• Chemical modification of histone tails can affect
  the configuration of chromatin and thus gene
  expression

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Histone Modification

• Histone acetylation (COCH3)seems to loosen
  chromatin structure and thereby enhance
  transcription

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DNA Methylation

• Addition of methyl groups to certain bases in
  DNA is associated with reduced transcription

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Eukaryotic Gene Regulation Control Elements

• Associated with most eukaryotic genes are
  multiple control elements - segments of noncoding
  DNA that help regulate transcription by binding
  certain proteins
• Distal control elements, groups of which are
  called enhancers may be far from a gene
• Regulatory molecules called activators can bind
  to regulatory enhancers to facilitate
  transcription factors

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Transcription Factors

• To initiate transcription, eukaryotic RNA
  polymerase requires the assistance of proteins
  called transcription factors
• General transcription factors are essential for
  the transcription of all protein-coding genes.
• Only a few general transcription factors
  independently bind to a DNA sequence such as the
  TATA box within the promoter.
• Others in the initiation complex are involved in
  protein-protein interactions, binding each other
  and RNA polymerase II.

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Regulation of Transcription Initiation

• In eukaryotes, regulatory molecules called
  activators can bind to regulatory enhancers

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Combinatorial Control of Gene Activation

• A particular combination of control elements will
  be able to activate transcription only when the
  appropriate activator proteins are present

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Repressors

• Some specific transcription factors function as
  repressors proteins inhibit expression of a
  particular gene
• Eukaryotic repressors can cause inhibition of
  gene expression by blocking the binding of
  activators to their control elements or to
  components of the transcription machinery or by
  turning off transcription even in the presence of
  activators.

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Post-transcriptional control

• Although less common than transcriptional control
  of gene expression, various types of
  posttranscriptional control may also occur in
  eukaryotes
• An increasing number of examples are being found
  of regulatory mechanisms that operate at various
  stages after transcription
• mRNA splicing
• mRNA degradation miRNA
• Protein degradation

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RNA Processing

• In alternative RNA splicing different mRNA
  molecules are produced from the same primary
  transcript, depending on which RNA segments are
  treated as exons and which as introns

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mRNA Degradation

• RNA interference by single-stranded microRNAs
  (miRNAs) can lead to degradation of an mRNA or
  block its translation

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Post translation

• After translation various types of protein
  processing, including cleavage and the addition
  of chemical groups, are subject to control
• Proteasomes are giant protein complexes that bind
  protein molecules and degrade them

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Cancer Biology

• Mutations are changes in the genetic material of
  a cell
• Mutations can occur during DNA replication,
  recombination, or repair
• Cancer results from genetic changes that affect
  cell cycle control
• Mutation of genes controlling cell division can
  lead to cancer
• The gene regulation systems can go wrong due to
• Chromosomal alterations - translocations
• Point mutations - Carcinogens
• Carcinogens are chemical or physical agents that
  interact with DNA to cause mutations leading to
  cancer
• Radiation - X-rays and ultraviolet light
• Chemicals arsenic, asbestos, benzene, ethanol,
  formaldehyde, gasoline
• Tumor viruses - transform cells into cancer
  cells through the integration of viral nucleic
  acid into host cell DNA.

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Cancer

• Cancer results from genetic changes that affect
  cell cycle control
• Cancer is the unregulated cell growth and
  division forming a cluster of cells forming a
  tumor that constantly expands in size
• Cells that leave the tumor, spread to other parts
  of the body, and form new tumors are called
  metastases

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Genes Associated with Cancer

• The genes that normally regulate cell growth and
  division during the cell cycle include genes for
• Growth Factors
• GF Receptors
• Intracellular molecules of signaling pathways
• Mutations altering any of these genes in somatic
  cells can lead to cancer
• Most human cancers result from mutations in one
  of two types of growth-regulating genes
• Proto-oncogenes code for proteins involved in
  stimulating cell division
• Tumor-suppressor genes code for proteins involved
  in inhibiting cell division

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Growth Factors and Cancer

• Proto-oncogenes code for proteins involved in
  stimulating cell division (e.g. growth factors,
  growth factor receptors, cyclins)
• Mutated proto-oncogenes that stimulate a cell to
  divide when it shouldnt are called oncogenes
  (cancer-causing genes).
• Tumor-suppressor genes code for proteins involved
  in inhibiting cell division
• Mutated tumor-suppressor genes that do not
  inhibit cell division when they should can also
  cause cancer.

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Cancer

• Proto-oncogenes are normal cellular genes that
  code for proteins that stimulate normal cell
  growth and division
• Oncogenes are cancer-causing genes
• A DNA change that makes a proto-oncogene
  excessively active, converts it to an oncogene,
  which may promote excessive cell division and
  cancer

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Ras protein

• The Ras protein, encoded by the ras gene, is a G
  protein that relays a signal from a growth factor
  receptor to a cascade of protein kinases
• Many ras oncogenes have a mutation that leads to
  a hyperactive Ras protein that issues signals on
  its own, resulting in excessive cell division

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p53 Gene - Tumor-suppressor Gene

• p53 inhibits cell division when DNA is damaged by
  stimulating transcription of p21. The p21
  protein then binds to cyclins and prevents them
  from binding with Cdk
• Abnormal p53 fails to stop division in cells with
  damaged DNA. If genetic damage accumulates as
  the cell continues to divide, the cell can turn
  cancerous.

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Cancer

• More than one somatic mutation is generally
  needed to produce a full-fledged cancer cell
• About a half dozen DNA changes must occur for a
  cell to become fully cancerous
• These changes usually include at least one active
  oncogene and mutation or loss of several
  tumor-suppressor genes

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Multistep Model of Cancer Development

• Colorectal cancer, with 135,000 new cases and
  60,000 deaths in the United States each year,
  illustrates a multistep cancer path

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Inherited Predisposition to Cancer

• The fact that multiple genetic changes are
  required to produce a cancer cell helps explain
  the predispositions to cancer that run in some
  families
• Individuals who inherit a mutant oncogene or
  tumor-suppressor allele have an increased risk of
  developing certain types of cancer

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Cancer

• Since cancer-causing mutations accumulate over
  time, cancer risk increases with age.