Explaining terms

 01.In silico cell

 02.Ion channels
 03.active transport
 04.ATP-powered pump
 05.Tight junctions
 06.Gap junctions
 07.Respiratory chain
 08.Nuclear pore complex
 09.Endomembrane system
 10.The cytoskeleton
 11.Elementary particle
 12.Signal peptide
 13.Nuclear pore
 14.Degenerate
 15.Cell cycle
 16.Homologus chromosome
 17.Sister chromatids
 18.Pars granulosa
 19.Hetero chromatin
 20.Meiosis
 21.Nuclearsome
Questions
 01.What are different between Eukaryotic cells and Prokaryotic cells ?
 02.Please explain the statement: plasma membrane is asymmetrical
membrane.
 03. What is the Fluid Mosaic Model ?
 04. Please explain the role of Cell junction and cell adhesion by use of
examples
 05.Comparing the difference in microtubule, microfilament, and
intermediate filament.
 06.Talk about the ultrastructure of mitochondria
 07.Mitochondria is called semiautonomous
organelle, why?
 08.Talk about the process that secretory proteins are synthesized and
transported
 09. The difference between mitosis and meiosis
 10. How many Checkpoints in cell cycle? What they check for?
 11. Describe the two kinds of molecular mechanism in apoptosis.
 12. Describe these 2 models of chromosome structure
 13. what’s the Signal theory for the translocation of protein?
 14. Describe the difference between apoptosis and Necrosis

Cell-Cycle Checkpoints
G1 Checkpoint
• �START in yeast
• �Restriction Point in mammals
• �Main step that commits a cell to division
• �Sensitive to:
• �� Cell size
• �� Availability of nutrients
• �� External growth factors
G2 checkpoint
�
Error check: DNA replication must be
complete
� Detects unreplicated DNA, holds cell at
G2
�� Detects damaged DNA, arrests cell in G2
until damage repaired
Spindle Assembly Checkpoint
• Boundary between metaphase and anaphase
• All chromosomes must be properly attached to the spindle
• MPF causes activation of anaphase promoting complex pathway that promotes
anaphase

In silico cell---------

Ion channels-------- Ion channels are usually small proteins that span the
membrane and have central water-filled pores and its outside surface is
hydrophobic and the inside hydrophilic. Most ion channels are gated and open
transiently in response to a specific stimulus, such as a change in membrane
potential or the binding of a ligand or a chemical (phosphorylation) or electrical
stimulus.
active transport------- Often the transport has to happen in the direction
opposite to the electrochemical or concentration gradient. In order to accom-
plish this, membranes have evolved elaborate schemes to pump the substance
( ions or moleciles) from the area of smaller concentration to a compartment
with higher concen-tration. All these schemes cost the cell energy (hydrolysis of
ATP or light energy) and thus are called active transport. It is sensitive to inhibi-
tors that stop ATP synthesis.
-

• ATP-powered pump------ ATP-powered pump is an ATPase that use the

energy of ATP hydrolysis to move ions or small molecules across a
membrane against a chemical concentration or electric potential gradient or
both. All ATP-powered pumps are transmembrane proteins with one or
more binding sites for ATP located on the cytosolic face of the membrane.
Although these proteins commonly are called ATPase, they normally do not
hydrolyze ATP into ADP and Pi unless ions or other molecules are
simultaneously transported.
•
•

• Tight junctions-------- Tight junctions, also called Occluding junctions, form

a physical barrier that prevents the leakage of even small molecules between
cells. Tight junctions are located between neighboring cells at the most
apical region of the cells and appear as points where the cell membranes
come into direct contact with each other. Tight junctions are composed of
anastomosing strands of transmembrane proteins that completely encircle
the cell. Tight junctions can regulate the passage of molecules across these
natural barriers. It restrict foodstuffs to the lumen and allow amino acids,
sugars, and other molecules, to be directly routed to the circulatory system.
•

• Gap junctions------- Gap junctions, such as the Communicating junctions,

attach cells together in a manner that allows the transfer of chemical or
electrical signals between neighboring cells. Gap junctions are formed by a
grouping of transmembrane proteins into a structure called a connexon.

Respiratory chain------- Respiratory chain is composed of a series of substance

which can accept and release electron or proton reversibly. They are a group of
lipid protein complex which are all existing on the inner membrane of
 mitochondria associatly and orderly, and coupling oxidative phosphorylation. So
respiratory chain can also be called electron transport chain.
Respiratory chain includes four complex
NADH-dehydrogenase complex ;
Succinate-CoQ dehydrogenase complex;
CoQ-cytochrome c dehydrogenase complex;
cytochrome c oxidase complex;

Nuclear pore complex-------- Nuclear pore structure is conferred by a set of

protein granule subunits, which are arranged in an octagonal pattern, and form
the boundaries of the pore complex.
It appears as if the two membranes are pinched at that site, leaving a space
filled with filamentous material. Sometimes a thin diaphragm may be seen
running horizontally through the pore. It contains 8 subunits that "clamp" over
region of the inner and outer membrane where they join. Actually, they form a
ring of subunits 15-20 nm in diameter. Each subunit projects a spoke-like unit
into the center so that the pore looks like a wheel with 8 spokes from the top.
Inside is a central "plug". The next (left) figure shows a cross section of the pore
with the clamp-like complex adjacent to the membranes. The projected spoke is
directed towards the central "plug' or granule.

• Endomembrane system------- The endomembrane system is a

collection of membranous structures involved in transport within the
cell. The main components of the endo-membrane system are the
endoplasmic reticulum, Golgi bodies, vesicles, lysosomes, peroxisomes
and nuclear envelope. These compartments are involved in the
processing of proteins for export from the cell, proteins destined for
lysosomes, and proteins entering the cell from the cell surface.
• Once proteins enter the endoplasmic reticulum they never return to
the cytosol compartment; they are carried by vesicle transport to the
other compartments of the system. This flow of vesicles is highly
regulated.

The cytoskeleton----------The cytoskeleton is that the maintenance of structure by

the cytosol arises from a complex network of protein filaments that traverse the cell
cytoplasm .

Elementary particle---------the elementary particle protein is composed of two

large oligomeric complexes. F0 is an integral membrane protein containing a, b,
c subunits. F1 is an peripheral protein that associates with the membrane
through F0. F1 contains nine subunits.

Signal peptide---------The mitochondrial signal peptides are stretches of 20 to 80

amino acids, at the NH2-terminus of the protein, that have the characteristic of
forming an amphipathic a-helix where one side of the helix is nonpolar and the
other side contains positively
charged amino acids. The signal peptide binds to a putative signal receptor on the
outer membrane , and the complex moves laterally across the outer membrane
until it reaches a contact site at which the inner and outer membranes are joined.

• Nuclear pore------- There are many small pores on the nuclear envelope
,which is called nuclear pore. It is formed by the two membranes fusion in
some places. The diameter of nuclear pore is about 40-100nm, average
diameter is 80nm.The number of nuclear pores is different with the cell type
and the physiological conditions. Nuclear pores allow communication
between the nucleus and cytosol.

Degenerate----------

Cell cycle-------------------

Homologus chromosome----------

Sister chromatids------------

Pars granulose-----------

Hetero chromatin-------------Heterochromatin is the condensed form of

chromatin organization. It is seen as dense patches of chromatin. Sometimes it
lines the nuclear membrane, however, it is broken by clear areas at the pores so
that transport is allowed. Sometimes, the heterochromatin forms a "cartwheel"
pattern. Abundant heterochromatin is seen in resting, or reserve cells such as
small lymphocytes (memory cells) waiting for exposure to a foreign antigen.
Heterochromatin is considered transcriptionally inactive.

Meiosis--------------Meiosis is a special type of nuclear division which segregates one

copy of each homologous chromosome into each new "gamete". It reduces the
number of sets of chromosomes by half, so that when gametic recombination
(fertilization) occurs the ploidy of the parents will be reestablished
 Nucleosome------------it is the lowest level of chromosome organization. The
fundamental histone-containing structural subunit of eukaryotic chromosomes. In
most eukaryotic organisms, nuclear deoxyribonucleic acid (DNA) is complexed with
an approximately equal mass of histone protein. The nucleosome is organized so that
the DNA is exterior and the histones interior. The DNA makes two turns around a
core of eight histone molecules
The nucleus is only 6 micrometers in diameter. The total length of DNA in the
human genome is 1.8 meters. Thus, in order to pack the DNA into the nucleus as
in the photograph of the metaphase chromosome , there must be several levels of
coiling and supercoiling. There is nearly a 10,000-fold reduction in length in an
interphase nucleus. Each chromosome contains 1 long molecule of DNA plus
associated histones (basic proteins) which help in the condensation and
regulation processes. These basic structures are known as nucleosome.
histone octomer + DNA = nucleosome

different between Eukaryotic cells and Prokaryotic cells

Prokaryotic cells Eukaryotic cells
size: 1-10µm size: 1-100µm
includes bacteria and blue- four major groups: Protista,
green algae fungi, plants and animals
no true nucleus true nucleus
DNA circular and free DNA linear and in nucleus
no membrane-bound internal compartmentalization
organelles with organelles, hence division of
labour (specialization)
simple binary reproduction mitotic reproduction(and meiotic)
no development of tissues tissue and organ systems common
multicellular types rare independent unicellular organism
or part of multicellular organism

Fluid mosaic model

The globular membrane proteins are embedded within the bilayer, with hydrophobic
portions of the proteins buried within the hydrophobic core of the lipid bilayer, and
hydrophilic portions of the proteins exposed to the aqueous environment, and the proteins
float within the lipid bilayer.

Role of Cell junction and cell adhesion

Cell adhesion plays a crucial role in embryogenesis, differentiation of adult tissues and
wound healing. The function and regulation of intercellular junction molecules in
desmosomes and adherens junctions act to mediate cell-cell adhesion and attachment of
the cytoskeleton to the cell surface.
Example 1 The importance of desmosomes in the maintenance of epithelial
integrity is underscored in human patients with the autoimmune disease pemphigus.
These patients produce autoantibodies that react specifically with the desmosomal
transmembrane linker glycoproteins. This disrupts desmosomes in the skin,
resulting in severe blistering and body fluid loss.
 • Example 2 A family of genetic (inherited) blistering diseases of the skin
that are caused by defective cell-ECM (cell extracellular matrix) adhesion.
EB is divided into three main categories based on where the loss of adhesion
occurs.
EB simplex junctional EB dystrophic EB
The 3 main types can be further sub-divided into at least 27 clinical variants.

difference in microtubule, microfilament, and intermediate filament

䦋㌌㏒ 䦋좈 ໱琰茞 microtubule microfilament Intermediate

ᓀ�Ü filament

component tubulin actin Intermediate

filament monomer

diametr 22nm 7nm 10nm

structure hollow tube two strands helix rope-strands helix

polarity yes yes no

treadmill action yes yes no

Ultrastructure of mitochondria
Outer membrane Outer membrane is the outerest unit membrane enveloping the
whole mitochondria. The width is 6nm. Its surface is smooth and elastical.
Inner membrane The inner membrane has a very large surface area owing to its
characteristic infolds ,which are called cristae. This membrane is composed of 75%
proteins and is extremely active functionally. The inner membrane contains proteins
involved in the respiratory chain ,ATP synthesis, and the transport of substrates
and products of oxidative phosphorylation into and out of the mitochondria.
The matrix contains enzymes involved in the oxidation of pyruvate and fatty acids
,as well as most of the enzymes of the citric acid cycle. In addition, the mitochondrial
genome and mitochondrial ribosomes are located in the matrix.
semiautonomous organelle- mitochondrion
 Mitochondria replicate much like bacterial cells. When they get too large, they
undergo fission. This involves a furrowing of the inner and then the outer
membrane as if someone was pinching the mitochondrion. Then the two daughter
mitochondria split. Of course, the mitochondria must first replicate their DNA. An
electron micrograph depicting the furrowing process is shown in these figures.
Mitochondria have their own autonomous double-stranded circular DNA, and
almost the entire genome is coding sequence. The human mitochondrial
genome contains 16569 nucleotides which encode 13 proteins, 2 rRNA genes
and 22 tRNA genes. Many of them are subunits of protein complexes involved
in electron transport and oxidative phosphorylation .
The difference
between mitosis and meiosis
䦋㌌㏒䦋좈໱琰茞 ᓀ
Mitosis Meiosis
�Ü

Number of divisions 1 2

Number of daughter
2 4
cells
Genetically identical? Yes No

Chromosome # Same as parent Half of parent

Where Somatic cells Germline cells
When Throughout life At sexual maturity
Role Growth and repair Sexual reproduction

Difference in apoptosis and necrosis

Apoptosis
• Chromatin condensation
• Cell Shrinkage
• Preservation of Organelles
and cell membranes
• Rapid engulfment by
neighboring cells
preventing inflammation
• Biochemical Hallmark:
DNA FRAGMENTATION
Necrosis
• Nuclear swelling
• Cell Swelling
• Disruption of Organelles
• Rupture of cell and release
of cellular contents
• Inflammatory response
2 models of chromosome structure
 Solenoid Model
of Chromosome Structure
first level : nuclearsome (packing ratio -7)

2nd level: 6 nulearsomes coiling into a helical array - 30nm solenoid (packaging
ratio -6)

3rd level : Solenoid coiling into a 400nm supersolenoid (packaging ratio -40)

4th level: chromotids (packaging ratio -5)

Scaffold-radial
loop structure
model

Two kinds of molecular mechanism in apoptosis

• Intrinsic/ Mitochondrial Apoptosis
– Regulated by Mitochondria
– Cytochrome c release
• Extrinsic/ Death Receptor Apoptosis
– Activated by ligation of Death Receptors
– Fas, TNF alpha
• These pathways intersect at the effector caspases.
 Intrinsic/Mitochondrial Pathway

Extrinsic/ Death Receptor apoptosis