Chapter 19 The Organization and Control of Eukaryotic Genomes

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Chapter 19The Organization and Control of
Eukaryotic Genomes
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Human Genome

• 3 billion base pairs.
• 30,000 to 50,000 genes.
• 3-5 active at any moment.

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Questions?

• With so much DNA in a cell, how is it organized
  or packaged?
• How is the expression of the DNA controlled?

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Movie DNA Packaging
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Microscopic Levels

• 1. Nucleosomes
• 2. 30-nm Chromatin Fibers
• 3. Looped Domains
• 4. Chromosomes

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Nucleosomes

• "Beads on a String.
• DNA wound on a protein core.
• Packaging for DNA.
• Controls transcription.

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Protein Core

• Two molecules of four types of Histone proteins.
• H1- 5th type of Histone protein attaches the DNA
  to the outside of the core.

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30 - nm Chromatin Fibers

• A cylinder of tightly coiled nucleosomes 30 - nm
  in diameter.

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Looped Domains

• Loops of 30 - nm chromatin.

Protein Scaffold
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Chromosomes

• Large units of DNA.
• Similar to "Chapters" in the Book of Life.

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Chromosome Regions

• 1. Heterochromatin - highly condensed chromatin
  areas that are not transcribed.
• 2. Euchromatin - less condensed chromatin areas
  of active transcription.

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Molecular Level Organization

• 1. Repetitive Sequences
• 2. Satellite DNA
• 3. Interspersed Repetitive DNA
• 4. Multigene Families

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Repetitive Sequences

• Tandemly repeating units of 1-10 nucleotides.
• 10 to 15 of total DNA.

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Satellite DNA

• Repetitive areas of DNA found at the
• Tips of chromosomes.
• Centromere regions.
• Structural DNA.

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Result

• Give regions of the DNA different densities.
• Linked to some genetic disorders.
• Ex. - Fragile X Syndrome
• Huntingtons disease

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Interspersed Repetitive DNA

• 25 - 40 of DNA
• Copies of repetitive units that are scattered
  among genes.
• Often transcribed, but function not
  clear.
• Ex. Alu elements.

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Multigene Families

• A collection of identical or very similar genes.
• From a common ancestral gene.
• May be clustered or dispersed in the genome.

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Types

• 1. Identical
• 2. Nonidentical

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Identical Families

• Identical genes for the same protein.
• Ex Ribosomal Protein and rRNA.
• Result - Many copies of ribosomes possible.
• Most common gene in DNA.

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Identical Genes
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Nonidentical Families

• Related clusters of genes that are nearly
  identical in their base sequences.
• Ex Globin Genes

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Globin Gene Evolution
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a - Globin Family

• Found on chromosome 16.
• Contains two copies of a globin, one
  fetal globin and four pseudogenes.

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b - Globin Family

• Found on chromosome 11.
• Contains two copies of b globin, one
  embryo, two fetal and one pseudogene.

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Pseudogene

• Gene with sequences very similar to real genes,
  but lack promoter sites.
• Are not transcribed into proteins.
• Possible proof of transpositions ?

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Genome Plasticity

• Changes in the ways a gene can be expressed.
• Seen only in somatic cells.
• Have major effects on gene expression within
  particular cells and tissues.

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Types

• 1. Gene Amplification
• 2. Selective Gene Loss
• 3. Genomic Rearrangements

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Gene Amplification

• The selective replication of certain genes.
• Ex rRNA genes in eggs
• Result - many copies of rRNA for making
  ribosomes.

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Selective Gene Loss

• Loss of genes or chromosomes in some tissues
  during development.
• Result - DNA (genes) lost and not expressed.

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Genomic Rearrangements

• Shuffling of DNA areas (not from Meiosis).
• Ex Transposons retrotransposons antibody
  genes.

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Transposons - Example
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Result

• Genes moved structurally within the genome.
• Transcription control changed.

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Control of Gene Expression

• Complicated Process.
• Many levels of control are possible.
• Hint - students should be able to discuss several
  mechanisms of control.

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Main Control Levels

• 1. Nucleus - those inside the nuclear membrane.
• 2. Cytoplasm - those that occur in the cytoplasm.

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Nucleus Level

• 1. Extra-Cellular Signals
• 2. Chromatin Modifications
• 3. Transcriptional Control
• 4. Posttranscriptional Control

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Extra-Cellular Signal

• Signal from outside the cells (usually a
  hormone).
• Review specifics from Chapter 11.
• Result - regions of DNA activated for
  transcription.

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Chromatin Modifications

• DNA Methylation.
• Histone Acetylation.
• Gene rearrangements.
• Gene amplification.

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DNA Methylation

• Addition of methyl groups (-CH3) to DNA
  bases.
• Result - long-term shut-down of DNA
  transcription.
• Ex Barr bodies genomic imprinting

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Histone Acetylation

• Attachment of acetyl groups (-COCH3) to AAs in
  histones.
• Result - DNA held less tightly to the
  nucleosomes, more accessible for transcription.

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Transcriptional Control

• Ex Enhancers, DNA-Binding
  Domains regulatory RNA.
• Result - genes are more (or less) available
  for transcription.
• Factors that affect the transcription of genes.

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Movie Turning on a Gene
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Enhancers

• Areas of DNA that increase transcription.
• May be widely separated from the gene
  (usually upstream).

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DNA-Binding Domains

• Proteins that bind to DNA and regulate
  transcription.
• Ex
• Helix-turn-Helix
• Zinc-Finger
• Leucine Zipper

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DNA Binding Domains
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Regulatory RNA

• Small RNA molecules that are not translated
• Interact with DNA
• Whole new area in gene regulation

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Posttranscriptional Control

• 1. RNA Processing Ex - introns
  and exons.
• 2. RNA Transport - moving the mRNA into the
  cytoplasm.
• 3. RNA Degradation - breaking down old mRNA.

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Transcription Control
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Movie RNA processing
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Cytoplasm Level of Control

• 1. Translation
• 2. Polypeptide Changes

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Movie Translation control
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Translation Control

• Regulated by the availability of initiation
  factors.
• Availability of tRNAs, AAs and other protein
  synthesis factors. (review Chapter 17).

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Polypeptide Changes

• Changes to the protein structure after
  translation.
• Ex Cleavage
• Modifications
• Activation
• Transport
• Degradation

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Movie Protein Processing
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Protein Degradation

• By Proteosomes using Ubiquitin to mark the
  protein.

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Gene Expression and Cancer

• Cancer - loss of the genetic control of cell
  division.
• Balance between growth-stimulating pathway
  (accelerator) and growth-inhibiting pathway
  (brakes).

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Proto-oncogenes

• Normal genes for cell growth and cell division
  factors.
• Genetic changes may turn them into oncogenes
  (cancer genes).
• Ex Gene Amplification, Translocations,
  Transpositions, Point Mutations

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Proto-oncogenes
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Tumor-Suppressor Genes

• Genes that inhibit cell division.
• Ex - p53, p21

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Cancer Examples

• RAS - a G protein.
• When mutated, causes an increase in cell division
  by over-stimulating protein kinases.
• Several mutations known.

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Cancer Examples

• p53 - involved with several DNA repair genes and
  checking genes.
• When damaged, cant inhibit cell division or
  cause damaged cells to apoptose.

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Comment

• p53 is known to be sensitive to cigarette smoke.
• Damage by smoke often leads to lung cancer.
• Over-activity of p53 causes problems too.

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Carcinogens

• Agents that cause cancer.
• Ex radiation, chemicals
• Most work by altering the DNA, or interfering
  with control or repair mechanisms.

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Multiple Hit Hypothesis

• Cancer is the result of several control
  mechanisms breaking down.
• Ex Colorectal Cancer requires 4 to 5 mutations
  before cancer starts.

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Colorectal Cancer
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Summary

• DNA packaging and gene expression are very
  complex with lots of opportunities for control
  points.
• Be able to discuss how DNA is organized and
  packed.

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Summary

• Be able to discuss mechanisms for regulating DNA
  and protein synthesis (know several ways)
• How control of DNA can lead to cancer.