Download Unit II: Chapter 12

I. The Genome
Figure 1: Human Genome
*The genome consists of 3.1 BILLION base pairs (bp’s) in gametes & 6.2 BILLION base pairs in body cells.
Figure 1.1: Genome “Reshuffling”
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Genome:
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Figure 2: DNA Packaging
(1) The lowest level of DNA packaging is the Nucleosome, consisting of a small amount of DNA wrapped 1¾ times
around an octamer of proteins called Histones. The combination of DNA & histone packing proteins is known as
Chromatin. Adjacent nucleosomes are connected by way of a small stretch of Linker DNA. In this way, the overall
structure of connected nucleosomes resembles beads on a string that shortens the length of the DNA. At its widest
point, the nucleosome has a diameter of 10 nm & is otherwise known as the 10nm Euchromatic Fiber.
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(2) Nucleosomes can be organized into a more compact structure or 30nm Euchromatic Fiber, which shortens the
total length of the DNA even more.
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(3) An additional level of chromatin compaction involves interactions between the 30nm fiber & the filamentous
network of proteins in the nucleus –these proteins are involved in compacting the DNA into Radial Loop Domains. The
distance that these loops radiate from the protein scaffold to which they connect is 300nm.
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(4) Chromatin that is organized into radial loop domains is regarded as Euchromatic, for it is “loosely” organized & is
therefore transcriptionally active. In some regions, however, the chromatin of chromosomes is further compacted via
the folding of the protein scaffold itself to form a fiber approximately 700nm in diameter. These Heterochromatic
regions are composed of repetitive DNA & are too “tightly” packed to be active.
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Figure 2.1: Interphase Chromosome Structure
*Chromatin is differentially packaged in interphase chromosomes, with some regions being euchromatic & others heterochromatic.
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The Centromere is a constricted region of a chromosome consisting of tightly coiled heterochromatin that contains
proteins (kinetochore complexes) that attaches to spindle fibers during division.
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Telomeres are at the ends of the chromosomes. They consist of many noncoding heterochromatic regions. The
noncoding sequences of telomeres exist to “protect” coding sequences from degradation (see chapter 16).
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Figure 2.2: Metaphase Chromosome Structure
During early stages of division, the entire chromosome compacts to the 700nm fiber & is regarded as heterochromatic
(genetically inactive). At this point, the entire chromosome has a diameter of 1400nm (2 chromatids x 700nm).
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Chromosome:
Figure 3: Chromosomes: Observed States During Cell Cycle
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Double Stranded Chromosomes:
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Single Stranded Chromosomes:
II. Mitotic Cell Division
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Mitosis:
a) The stages through which cells pass from one mitotic division to the next is called the Cell Cycle. The cell cycle
consists of 2 main phases: interphase & the M phase.
Figure 4: Cell Cycle: Interphase (G1, S, G2)
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Interphase:
a) G1 phase (1st Gap): is the longest phase of interphase characterized as a period of intense growth & metabolic
activity. Various organelles are replicated to ensure the resultant daughter cells are fully equipped to carry on all
life processes.
b) S phase (Synthesis): period during which the cell’s genome is replicated to ensure that each resultant daughter cell
has the same quantity & types of genes as the parent cell. Centrosome (& centrioles) replicate.
c) G2 phase (2nd Gap): period during which final preparations are made for division.
d) G0 phase (Quiescent Stage): stage at which a cell is considered to be “resting” (not preparing to divide). Most cells
will spend some time in G0, with the amount of time varying with cell type. Cells with low rates of division spend
large amounts of time in G0 until they are stimulated to divide. Others exhibit high rates of division & rarely enter
G0. Some cells, such as neurons of the CNS & muscle cells, permanently remain in G0; the cessation of division acts
to preserve neural & muscular networks that would be disrupted by further proliferation.
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Figure 4.1: Cell Cycle: M Phase (PPMAT)
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M Phase:
Figure 4.2: M Phase: Interphase - Prometaphase
Prophase: with the aid of a class of enzymes called Condensins, chromosomes coil into 46 Dyads (double stranded),
causing the nucleolus to disappear. Centrosomes (centrioles) migrate toward opposite poles of the cell, propelled along
the surface of the nucleus as polar microtubule fibers elongate to form the beginnings of a Mitotic Spindle (fig 4.3).
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Prometaphase: nuclear envelope fragments & the formation of the spindle is complete. Specialized regions within the
centromeres of the dyads called Kinetochores (fig 4.4) “capture” microtubules of the spindle. Once attached, the 46
dyads can begin migrating toward the spindle’s center …
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Figure 4.3: M Phase: Spindle Expansion (Prophase)
Figure 4.4: M Phase: Chromosome Spindle Attachment (Prometaphase)
*The kinetochore region enables each chromosome to attach to the spindle. This ultimately results in the dyads aligning along the
center of the spindle. Once aligned, the dyads are separated into single-stranded chromosomes.
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Figure 4.5: M Phase: Chromosome Spindle Migration (Prometaphase)
Once attached to a spindle (kinetochore) fiber, a kinetochore assumes an “active” state in which it depolymerizes
(breaks down) the fiber. This causes the chromosome to be pulled toward one of the centromeres. As it approaches,
the chromosome encounters additional fibers growing from the centromere. This causes the kinetochore to assume a
“passive” state in which it re-polymerizes the fiber, allowing it to slide along the growing fiber as it gets pushed away
from the centrosome …
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Ultimately, the pushing forces generated by spindle fibers emanating from each centrosome will be the same on both
sides of the chromosome. At this point, the chromosome will lie along an imaginary plane of the spindle apparatus
called the Metaphase Plate …
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Figure 4.5: M Phase: Metaphase - Telophase
Metaphase: the interaction between kinetochore fibers & spindle microtubules, enables all 46 dyads to line up on the
Metaphase Plate, an imaginary plane equidistant from both poles.
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Anaphase: during a process known as Disjunction, the chromatids of each dyad separate at their centromere to form
Single-Stranded Chromosomes, which begin to move toward opposite poles of the cell. Each pole of the spindle now
has a complete set of 46 single stranded chromosomes (equal’s amount of genetic material in the parent cell at G1).
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Figure 4.6: M Phase: Disjunction (Anaphase)
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Telophase: karyokinesis (nuclear division) concludes as the cell continues to elongate & the nuclear envelope reforms
from fragments of the original envelope of the parent cell. The cell now contains two genetically identical nuclei, each
containing 46 single-stranded chromosomes, which decondense back into their interphase state (nucleolus reappears).
Before telophase is completed, Cytokinesis, the division of cytoplasm commences …
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Figure 4.7: Cytokinesis: Animal vs Plant Cells
Cytokinesis: is the splitting of the cytoplasm to produce two free-living daughter cells. Although each daughter cell
may differ in size & shape, they are genetically identical to each other & the original parent cell (2n to 2n). The means
by which this process occurs differs in animal & plant cells:
a) Animal Cells: a Contractile Ring consisting of actin fibers & myosin motor proteins forms on the cytoplasmic side
of the plasma membrane. It contracts to form a Cleavage Furrow that deepens to ultimately pinch cell in two.
b) Plant Cells: cytokinesis involves the formation of a Cell Plate formed from the merging of vesicles derived from the
Golgi apparatus that contain cellulose synthesizing enzymes. These vesicle collect & merge within a narrow,
microtuble–based complex called a Phragmoplast. This results in the formation of a membrane called a Cell Plate
within which are embedded cellulose synthesizing enzymes for the formation of a cell wall.
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Prokaryotic Cell Division
Figure 5: Binary Fission
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Binary Fission:
Figure 5.1: Prokaryotic Genetic Recombination
Conjugation: bacterial cells join together via a cytoplasmic bridge called a Sex Pilus. This allows for the direct
exchange of small circular DNA fragments called Plasmids that may contain genes beneficial to survival (e.g. antibiotic
resistance genes).
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Transformation: bacterial cells may absorb free DNA from their surroundings, such as those released by a neighboring
cell that has died & disintegrated. Incorporation of these new genes may provide traits beneficial in times of stress.
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Transduction: bacterial cells may obtain bacterial DNA from a viral particle that, during its formation within another
bacterial host, incorporated bacterial DNA inside is capsule instead of viral DNA.
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V. Control of the Cell Cycle
Figure 6: Cell Cycle Control: Cdk’s & Cyclins
The interaction between Cyclin-Dependent Kinases (Cdk’s) & Cyclins ensures that events associated with the cell
cycle occur in a specific, sequential manner (G1 S G2 M).
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Cyclins are proteins whose concentration steadily increase throughout the cell cycle. Upon reaching a maximum
concentration, cyclins attach to their conjugate Cyclin-Dependent Kinase (Cdk) to form an active complex. Once
active, the cyclin-Cdk complex initiates specific events within each phase of the cell cycle. In fig. 6, the mitotic cdkcyclin complex initiates the events from prophase to metaphase (e.g. chromosome condensation, spindle formation,
chromosome spindle attachment & alignment, etc.). The events within each phase of the cell cycle is controlled by a
specific cyclin-Cdk complex.
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The last event initiated by a cyclin-Cdk complex is the activation of enzymes that degrade the cyclin, causing the Cdk
to revert to its original inactive state. This signals the end of a particular cell cycle phase & allows the cell to pass into
the next phase.
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Figure 6.1: Major Cdk’s & Cyclins
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Figure 6.2: Stimulating the Cell Cycle: Growth Factors
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Growth factors or Mitogens are secretory proteins that stimulate cells to leave G0 & enter the cell cycle.
Growth factors stimulate cyclin synthesis in order to initiate the cell cycle (G1  M).
Different cell types are stimulated to enter G1 (from G0) by a specific growth factor/mitogen.
Figure 6.3: Effects of Growth Factors (Platelet-Derived Growth Factor)
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Figure 6.5: Inhibiting the Cell Cycle: Density-Dependent Inhibition
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Density-Dependent Inhibition:
Figure 6.6: Inhibiting the Cell Cycle: Anchorage Dependence
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Anchorage Dependence:
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Cell Cycle Checkpoints
Figure 7: Major Checkpoints
Within each stage of the cell cycle, specialized protein act to serve as Checkpoints to monitor the integrity of the
cell’s DNA. These checkpoints primarily deal with “checking” for DNA damage & the proper connection & alignment of
chromosomes along the spindle:
a) G1 Checkpoint (Restriction Point): checks for DNA damage prior to the S Phase to prevent it from being replicated.
Any DNA damage sustained during this phase will trigger kinases to arrest the cell in G1. DNA repair pathways will
be activated to repair the damage (or apoptosis if damage is too extensive).
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Figure 7.1: G1 Checkpoint
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b) Intra S Checkpoint: DNA damage or mistakes in DNA replication trigger kinases to arrest the cell in S. DNA repair
pathways will be activated to repair the damage (or apoptosis if damage is too extensive).
c) G2 Checkpoint: DNA damage or mistakes in DNA replication kinases to stimulate G2 arrest. DNA repair pathways
will be activated to repair the damage (or apoptosis if damage is too extensive).
d) M (Spindle) Checkpoint: consists of proteins that prevent cells from entering anaphase until chromosomes are
properly attached to the spindle. These proteins form an inhibitory complex around the cyclin CDC20, preventing
it from associating with the Anaphase Promoting Complex (APC). Only when ALL chromosomes are properly
attached to the spindle is this cyclin released from the inhibitory complex & the APC is activated. When active, the
APC initiates events leading to the destruction of the cohesins binding sister chromatids to facilitate their
separation. It also triggers the degradation of cyclins that stimulate MPF & activates the synthesis of G1 cyclin for
the next turn of the cycle.
Figure 7.2: M Checkpoint: CDC20 & APC
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VI. Mitosis & Cancer
Figure 8: Proto / Oncogenes
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Oncogenes:
a) All oncogenes produce products that are always active or produce a product in excess (i.e. cyclins) As a result, the
rate of the cell cycle increases which can lead to the progressive accumulation of additional oncogenes.
b) Oncogene development leads in the formation of defective checkpoint proteins (i.e P53). As a result, checkpoints
breakdown & allow the defective cells to divide  cancerous growths / tumors.
c) Malignant tumors are those whose cells detach from the primary mass whereby they may enter the circulatory or
lymphatic system during a process called Metastasis.
Figure 8.1: Tumor Metastasis
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Figure 8.2: Oncogenes & Cancer
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Cancer:
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