CHAPTER 24 Genes and Chromosomes

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CHAPTER 24 Genes and Chromosomes
Key topics

• Organization of information in chromosomes
• DNA supercoiling
• Structure of the chromosome

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Management and Expression of Genetic Information

• Previous chapters dealt with
• metabolic pathways, in which the chemical
  structures of small molecules were modified by
  enzymes
• signal transduction pathways, in which
  interactions of ligands with receptor proteins
  caused physiological responses
• The following chapters deal with
• information pathways, in which genetic
  information stored as the nucleotide sequence is
  maintained and expressed

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The Central Dogma of Molecular Biology

• The discovery of double-helical structure of DNA
  in 1953 laid a foundation to thinking of
  biomolecules as carriers of information
• It was well understood by 1950 that proteins play
  roles of catalysts but their role in information
  transfer was unclear
• Francis Crick proposed in 1956 that Once
  information has got into a protein it cant get
  out again
• The Central Dogma was proposed by Francis Crick
  at the time when there was little evidence to
  support it, hence the dogma

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How does genes function? Central Dogma DNA to
RNA to Protein.
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Genes and Chromosomes

• What is gene?
• One gene-one enzyme.
• One gene-one protein (polypeptide).
• Genes are segments of DNA that code for
  polypeptides and RNAs.
• What is chromosome?
• Chromosome consists of one covalently connected
  DNA molecule and associated proteins
• Viral genomic DNA may be associated with capsid
  proteins
• Prokaryotic DNA is associated with proteins in
  the nucleoid
• Eukaryotic DNA is organized with proteins into a
  complex called the chromatin

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DNA is a Very Large Macromolecule

• The linear dimensions of DNA are much bigger than
  the virions or cells that contain them
• Bacteriophages T2 and T4 are about 0.2 ?m long
  and 0.1 ?m wide
• Fully extended T4 DNA double helix is about 60 ?m
  long
• DNA in the virion or cell is organized into
  compact forms, typically via coiling and
  association with proteins

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The Size and Sequence of DNA Molecules in
Bacteria and their viruses
Bacteria(E. coli) 4,639,221 1.7 mm
0.002 mm
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T2 phage
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The sizes of E. coli cell and its DNA
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DNA from a lysed E. coli cell
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DNA, Chromosomes, Genes, and Complexity

• Note that despite the trends in the previous
  table, neither the total length of DNA, nor the
  number of chromosomes correlates strongly with
  the perceived complexity of the organisms
• Amphibians have much more DNA than humans
• Dogs and coyotes have 78 chromosomes in the
  diploid cell
• Plants have more genes than humans
• The correlation between complexity and genome
  size is poor because most of eukaryotic DNA is
  non-coding
• Recent experimental work by Craig Venter suggests
  that a minimal living organisms could get by with
  less than 400 genes

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DNA content and C-value paradox
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Eukaryotic genomes have several sequence
components

• Nonrepetitive DNA the complexity of the slow
  component corresponds with its physical size,
  i.e., unique sequences.
• Moderately repetitive DNA.component with a
  Cot1/2 of 10-2 and that of nonrepetitive DNA.
  Contains families of sequences that are not
  exactly the same, but are related. The complexity
  is made up of a variety of individual sequences,
  each much shorter, whose total length together
  comes to the putative complexity. Usually
  dispersed throughout the genome.
• Highly repetitive DNA component which
  reassociates before a Cot1/2 of 10-2. Usually
  forms discrete clusters.

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Types of sequences in the human genome
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Composition of the Human Genome

• Notice that only a small fraction (1.5 ) of the
  total genome encodes for proteins
• The biological significance of non-coding
  sequences is not all clear
• Some DNA regions directly participate in the
  regulation of gene expression (promoters,
  termination signals, etc)
• Some DNA encodes for small regulatory RNA with
  poorly understood functions
• Some DNA may be junk (pieces of unwanted genes,
  remnants of viral infections

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Many eukaryotic genes contain intervening
sequences (introns)
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Some Bacterial Genomes Also Contain Introns

• It was thought until 1993 that introns are
  exclusive feature of eukaryotic genes
• About 25 of sequenced bacterial genomes show
  presence of introns
• Introns in bacterial chromosome do not interrupt
  protein-coding sequences they interrupt mainly
  tRNA sequences
• Introns in phage genomes within bacteria
  interrupt protein-coding sequences
• Many bacterial introns encode for catalytic RNA
  molecules that have ability to insert and reverse
  transcribe themselves into the genomic DNA

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Transposons

• DNA sequence is not completely static
• Some sequences, called transposons, can move
  around within the genome of a single cell
• The ends of transposons contain terminal repeats
  that hybridize with the complementary regions of
  the target DNA during insertion
• To be covered in Ch. 25.

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Eukaryotic Chromosomes
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Important Structural Elements of the Eukaryotic
Chromosome

• Telomeres cap the ends of linear chromosomes and
  are needed for successful cell division
• Centromere functions in cell division thats
  where the two daughter chromosomes are held
  together during mitosis (i.e. after DNA
  replication but before cell division)

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Centromere Mitotic segregation of chromosomes.
Simple-sequence DNA is located at centromere in
higher eukaryotes. Telomere At ends of
chromosomes. (TTAGGG)n in human.
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Telomeres and Cellular Aging

• In many tissues, telomeres are shortened after
  each round of replication (end-replication
  problem of linear DNA) the cellular DNA ages
• Normal human cells divide about 52 times before
  losing ability to divide again (Hayflick limit)

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How is DNA packed in the chromosomes

• DNA Supercoiling.
• Proteins assisted packaging (nucleosomes)

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DNA Supercoiling

• DNA in the cell must be organized to allow
• Packing of large DNA molecules within the cells
• Access of proteins to read the information in DNA
  sequence
• There are several levels of organization, one of
  which is the supercoiling of the double-stranded
  DNA helix

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Supercoils
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Supercoiling of DNA can only occur in
closed-circular DNA or linear DNA where the ends
are fixed.
Underwinding produces negative supercoils, wheres
overwinding produces positive supercoils.
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Negative and positive supercoils .
Topoisomerases catalyze changes in the linking
number of DNA.
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Supercoiling induced by separating the strands of
duplex DNA (eg., during DNA replication)
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Relaxed and supercoiled plasmid DNAs
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Negative supercoils facilitate separation of DNA
strands (may facilitate transcription)
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Topology of cccDNA is defined by Lk Tw Wr,
where Lk is the linking number, Tw is twist and
Wr is writhe.
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Intertwining of the two strands

• Nodes ss crossing on 2D projection.

Right-handed crossing 1/2
Left-handed crossing -1/2
Lk number of times one strand winds around the
other on 2D projection. One linking number 2
nodes.
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Promotion of cruciform structures by DNA
underwinding
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Mechanism of Type I topoisomerase action
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Proposed mechanism of Type II topoisomerase action
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Topoisomerases are Targets for Antibiotics and
Anti-cancer Drugs
Bacterial topoisomerase inhibitors
Type I topoisomerase inhibitors
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Human Type II topoisomerase inhibitors
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DNA damages are produced by topoisomerase
inhibitors

• Most topoisomerase inhibitors act by blocking the
  last step of the topoisomerase reaction, the
  resealing of the DNA strand breaks. Therefore,
  these inhibitors will produce single-strand or
  double-strand DNA breaks in the DNA.

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Plectonemic supercoiling
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DNA Compaction Requires Solenoidal Supercoiling,
not plectonemic supercoiling.
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Changes in chromosome structure during the cell
cycle
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Protein-assisted Packaging of DNA Nucleosomes are
the fundamental organizational units of
eukaryotic chromatin
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Each nucleosome has a histone core wrapped by DNA
(146 bps) in a left-handed solenoidal supercoil
about 1.8 times. The linker DNA is about 54 bps
in length.
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DNA wrapped around a nucleosome core
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Histones are small, basic protein. The histone
core in nucleosomes contains two copies each of
H2A, H2B, H3 and H4. Histone H1 binds to linker
DNA.
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Chromatin assembly
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Nucleosomes are packed into successively
higher-order structures
The 30 nm fiber, a higher-order organization of
nucleosomes.
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A partially unraveled human chromosome, revealing
numerous loops of DNA attached to scaffold.
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Higher order of folding is not yet understood.
Certain regions of DNA are associated with a
nuclear scaffold. The scaffold associated regions
are separated by loops of DNA with 20 to 100 kb
long.
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Model of DNA compaction in eukaryotic chromosomes
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Condensed chromosome are maintained by SMC
proteins
SMC Proteins
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Model for the effect of condensins on DNA
supercoiling