Cells and genome

S2 IKD & Biomedis

Matakuliah Biologi Sel dan Molekuler
September – Desember 2011
 Cell is a closed compartment, separated from
extracellular space by cell membrane, consists of cytosol
and intracellular organelles

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 Nucleus is the center of information storage in cell

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Figure 4-9 Molecular Biology of the Cell (© Garland Science 2008)
 The information is written in
“molecular letters” called nucleotide

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Nucleotides are joined together to
form “linear code” called nucleic acid
• Nucleotides are joined together
by a phosphodiester linkage
between 5’ and 3’ carbon atoms
to form nucleic acids.

• The linear sequence of

nucleotides in a nucleic acid
chain is commonly abbreviated
by a one-letter code, A—G—C—
T—T—A—C—A, with the 5’ end
of the chain at the left.

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 DNA is a double stranded nucleic acid
The bases of one strand pair with bases in the
complementary strand

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The double stranded DNA form a helix

The members of each base pair

can fit together within the double
helix only if the two strands of the
helix are antiparallel

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 The information in the nucleus is divided into
several “books” (chromosomes)

Chromosomes are DNA molecules

that can be observed individually in
cells only during mitosis

In cells during interphase, the DNA

is in uncondensed state and difficult
to be distinguished

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Figure 4-11 Molecular Biology of the Cell (© Garland Science 2008)
 The “books” (chromosomes) are divided into
many “chapters” (genes)

However, there are

many regions of DNA
that do not encode any
protein (non gene)

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Figure 4-15 Molecular Biology of the Cell (© Garland Science 2008)
 Gene is a “recipe” to synthesize a protein
It consists of regulatory sequence (promotor), exons and introns
The gene is expressed when when this “document” is used to synthesize a
protein. When it is not used to synthesized a protein, the gene is term as
silence

Protein is made in the

ribosomes

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Figure 4-15 Molecular Biology of the Cell (© Garland Science 2008)
 There are very long DNA strand inside a nucleus

Figure 4-16 Molecular Biology of the Cell (© Garland Science 2008)

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Table 4-1 Molecular Biology of the Cell (© Garland Science 2008)
How can such long DNA can be fitted
inside a tiny chamber of nucleus?

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 Eukaryotic chromosomes consist of repeated units of
chromatin called nucleosomes

Nucleosome is discovered by chemically digesting cellular nuclei and stripping away as much of the
outer protein packaging from the DNA as possible. The chromatin that resisted digestion had the
appearance of "beads on a string" in electron micrographs — with the "beads" being nucleosomes
positioned at intervals along the length of the DNA molecule

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Figure 4-22 Molecular Biology of the Cell (© Garland Science 2008)
Nucleosomes are made up of double-stranded DNA that has
complexed with small proteins called histones

Each nucleosome contains eight histone proteins (blue), and DNA wraps
around these histone structures to achieve a more condensed coiled form

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 The multiple levels of
packing within eukaryotic
chromosomes permit a large
amount of DNA to occupy a
very small space

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Figure 4-72 Molecular Biology of the Cell (© Garland Science 2008)
The multiple levels of packing within eukaryotic chromosomes
serve several functional roles in controlling gene expression

• Highly compacted chromatin simply isn't accessible to the enzymes

involved in DNA transcription, replication and repair

– Euchromatin, regions of chromatin where active transcription is

taking place are less condensed
– Heterochromatin, regions where transcription is being inactive or
repressed are highly condensed

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What is genome?

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During cell proliferation cycle, the chromosomes can be
replicated and divided equally into two daughter cells

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In addition to nucleus, eukaryotic cells contain
intracellular organelles
Each organelles
performs a specific function critical to the cells’s survival
and is separated from each other by a membrane
(therefore they sometimes called the endomembrane system)

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 Cells consist of endomembrane system

• Nuclear envelope
• Endoplasmic Reticulum
• The Golgi Apparatus
• Lysosomes
• Peroxisome
• Vesicles

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 Nuclear envelope consists of inner and outer membrane which
are continuation of the membrane of endoplasmic reticulum

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Figure 12-8 Molecular Biology of the Cell (© Garland Science 2008)
 Endoplasmic Reticulum (ER):
the production center or factories of the cells
• Rough ER
– has many ribosomes attached in
their membrane
– transports newly formed protein
to Golgi apparatus
– inside the lumen of Rough ER,
proteins can be chemically
modified

• Smooth ER
– is the site of detoxification of
chemically modifying small
molecules (drugs and pesticides)
– the site for the hydrolysis of
glycogen in animal cells
– the site for the synthesis of lipids
and steroids

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 Golgi Apparatus:
the packaging facilities of cell products

• Golgi apparatus
– receives proteins from the ER and may further modify them
– concentrates, packages, and sorts proteins before they are sent to their
cellular or extracellular destinations

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Figure 13-26 and 13-25 Molecular Biology of the Cell (© Garland Science 2008)
 Vesicles:
package of substance that can be delivered from one
compartment to other compartment inside a cell

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Figure 13-2 Molecular Biology of the Cell (© Garland Science 2008)
 • Lysosomes the
digestion center of the cells
– are sites for the
breakdown of food and
foreign objects taken up
by the cell by
phagocytosis
– are sites where the cell
digests its own material
(autophagy)

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 Peroxisomes: minor digestion and detoxification

– are spherical organelles

– contain digestive and
detoxifying enzymes
– produce hydrogen peroxide
as a byproduct

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Figure 12-30 Molecular Biology of the Cell (© Garland Science 2008)
 Mitochondria:
Center of energy production

• A mitochondrion is bounded by
two membranes: a smooth
outer membran amd inner one
which is folded into numerous
contiguous layers called cristae

• The cristae partition the mitochondrion into

two compartments: a matrix, lying inside the
inner membrane; and intermembrane space

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Figure 12-21 Molecular Biology of the Cell (© Garland Science 2008)
 Mitochondria have circular DNA in the matrix and may
produce protein inside the organelles. However, they also
imported proteins encoded by nuclear genes

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Figure 14-53 Molecular Biology of the Cell (© Garland Science 2008)
Cytosol is not a liquid compartment but more resemble
gel-like structure
Many filaments can be found in the cytosol

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 Microtubule, intermediate filament, microfilament
are the main cytoskeleton of the cell
What is the function of cytoskeleton?

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Figure 1-30 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
Microtubules are hollow tubes of 25 nm in
diameter

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 Microtubules are formed by polymerization of
tubulin dimer

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Figure 16-11 Molecular Biology of the Cell (© Garland Science 2008)
 Tubulin polymerization is started in a region
near nucleus called centrosome

Centrosome consists
of a pair of centrioles

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Figure 16-31a Molecular Biology of the Cell (© Garland Science 2008) Figure 16-30a Molecular Biology of the Cell (© Garland Science 2008)
 Microtubules
bind to many
accessory
proteins

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Microfilament is the is the thinnest
cytoskeleton filament

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 Microfilaments are formed by many
globular actin subunits

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Figure 3-24 Molecular Biology of the Cell (© Garland Science 2008) Figure 3-25 Molecular Biology of the Cell (© Garland Science 2008)
 Actin
cytoskeleton
binds to many
accessory
proteins

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 Microfilament may form contractile or non contractile
bundles

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Figure 16-49a Molecular Biology of the Cell (© Garland Science 2008)
 Some drugs affect actin filament and microtubules

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Table 16-2 Molecular Biology of the Cell (© Garland Science 2008)
 Intermediate filament got its name because its
diameter is in between diameter of microtubules
and microfilament

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 Intermediate filament is formed by fibril subunits

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Figure 16-19 Molecular Biology of the Cell (© Garland Science 2008)
 Detection of intermediate filament expression may be
used to differentiate type of cells

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Table 16-1 Molecular Biology of the Cell (© Garland Science 2008)
 The cell structure

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Figure 1-30 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008)
 Thank you

S2 IKD & Biomedis

Matakuliah Biologi Sel dan Molekuler
September – Desember 2011