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How does a cell know what function it has within an organism?

How does a cell know what function it has within an organism?



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Given that all cells in a multicellular organism contain the same DNA (ignoring random mutations during mitosis), how does any given cell know what purpose it is supposed to have within an organism.

For example, how does a cell know to become a muscle cell, a neuron or a liver cell?


The answer to this question can be split into two parts: cell differentiation from stem cells and simple mitosis. Also, the answer I am providing mainly only applies to species that sexually reproduce.

During the primary stages of growth, immediately following the fertilisation of the female gamete, the zygote begins to divide. Most of these initial cells will not be specialised, they will be stem cells and these have the potential to asymmeterically divide. When they do this, each of the daughter cells will have a specific specialisation path to follow. Which path they will follow, muscular, neural etc. is determined by transcription proteins.

Once the stem cells have produced the correct daughter cells, the general structure of the organism will begin to take form. Once this happens and the cells have followed their development paths until they hit their final specialisation, mitosis takes over. This means that a muscle cell will divide, causing the organism to grow. A muscle cell, will only ever divide into a muscle cell, the same goes for all specialised cells. This is how an organism grows and maintains itself.

However, some stem cells do remain after the organism has matured. For instance, a mature neuron is unable to undergo mitosis, so stem cells are needed to allow for the production of new neurons to replace those that die, to take one example.

You can find out more here.


How does a cell know what function it has within an organism? - Biology

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cell, in biology, the basic membrane-bound unit that contains the fundamental molecules of life and of which all living things are composed. A single cell is often a complete organism in itself, such as a bacterium or yeast. Other cells acquire specialized functions as they mature. These cells cooperate with other specialized cells and become the building blocks of large multicellular organisms, such as humans and other animals. Although cells are much larger than atoms, they are still very small. The smallest known cells are a group of tiny bacteria called mycoplasmas some of these single-celled organisms are spheres as small as 0.2 μm in diameter (1μm = about 0.000039 inch), with a total mass of 10 −14 gram—equal to that of 8,000,000,000 hydrogen atoms. Cells of humans typically have a mass 400,000 times larger than the mass of a single mycoplasma bacterium, but even human cells are only about 20 μm across. It would require a sheet of about 10,000 human cells to cover the head of a pin, and each human organism is composed of more than 30,000,000,000,000 cells.

What is a cell?

A cell is a mass of cytoplasm that is bound externally by a cell membrane. Usually microscopic in size, cells are the smallest structural units of living matter and compose all living things. Most cells have one or more nuclei and other organelles that carry out a variety of tasks. Some single cells are complete organisms, such as a bacterium or yeast. Others are specialized building blocks of multicellular organisms, such as plants and animals.

What is cell theory?

Cell theory states that the cell is the fundamental structural and functional unit of living matter. In 1839 German physiologist Theodor Schwann and German botanist Matthias Schleiden promulgated that cells are the “elementary particles of organisms” in both plants and animals and recognized that some organisms are unicellular and others multicellular. This theory marked a great conceptual advance in biology and resulted in renewed attention to the living processes that go on in cells.

What do cell membranes do?

The cell membrane surrounds every living cell and delimits the cell from the surrounding environment. It serves as a barrier to keep the contents of the cell in and unwanted substances out. It also functions as a gate to both actively and passively move essential nutrients into the cell and waste products out of it. Certain proteins in the cell membrane are involved with cell-to-cell communication and help the cell to respond to changes in its environment.

This article discusses the cell both as an individual unit and as a contributing part of a larger organism. As an individual unit, the cell is capable of metabolizing its own nutrients, synthesizing many types of molecules, providing its own energy, and replicating itself in order to produce succeeding generations. It can be viewed as an enclosed vessel, within which innumerable chemical reactions take place simultaneously. These reactions are under very precise control so that they contribute to the life and procreation of the cell. In a multicellular organism, cells become specialized to perform different functions through the process of differentiation. In order to do this, each cell keeps in constant communication with its neighbours. As it receives nutrients from and expels wastes into its surroundings, it adheres to and cooperates with other cells. Cooperative assemblies of similar cells form tissues, and a cooperation between tissues in turn forms organs, which carry out the functions necessary to sustain the life of an organism.

Special emphasis is given in this article to animal cells, with some discussion of the energy-synthesizing processes and extracellular components peculiar to plants. (For detailed discussion of the biochemistry of plant cells, see photosynthesis. For a full treatment of the genetic events in the cell nucleus, see heredity.)


In complex organisms, tissues grow by simple multiplication of cells. This takes place through the process of mitosis in which the parent cell breaks down to form two daughter cells identical to it. Mitosis is also the process through which simpler organisms reproduce and give rise to new organisms.

Cells import nutrients to use in the various chemical processes that go on inside them. These processes produce waste which a cell needs to get rid of. Small molecules such as oxygen, carbon dioxide and ethanol get across the cell membrane through the process of simple diffusion. This is regulated with a concentration gradient across the cell membrane. This is known as passive transport. However, larger molecules, such as proteins and polysaccharides, go in and out of a cell through the process of active transport in which the cell uses vesicles to excrete or absorb larger molecules.


Cell Structures

The Nucleus

  • Usually found at center of cell
  • Has a nuclear membrane nuclear pores
  • Contains cell's DNA in one of 2 forms
    • chromatin- DNA bound to protein (non-dividing cell)
    • chromosomes- condesed structures seen in dividing cell

    Mitochondria

    Energy center or "powerhouse" of the cell. Turns food into useable energy (ATP)

    Ribosome - make protein, located on the rough endoplasmic reticulum and throughout the cytoplasm

    Golgi Apparatus - processing, packages and secretes proteins proteins are transported in vesicles

    Lysosome - contains digestive enzymes that can break things down, also called a "suicide sac" because the rupturing of the lysosome will cause the cell to destroy itself

    Endoplasmic Reticulum - Transport, "intracellular highway". Ribosomes are positioned along the rough ER, protein made by the ribosomes enter the ER for transport.

    Smooth ER - no ribosomes
    Rough ER - contains ribosomes

    Cytoskeleton - helps maintain the cells shape supports the cell and aids in cell movement

    microtubules / microfilaments / centrioles

    microtubules are used to build cilia and flagella

    Vacuole - storage area for water and other substances, plant cells usually have a large central vacuole


    Pattern Formation

    During morphogenesis, a process called pattern formation drives the spatial organization of tissues and organs into a defined body plan, or final shape. For example, both dogs and humans have legs made up of bone, muscle, and skin. During development, differentiation produces muscle cells, bone cells, and skin cells from an unspecialized set of embryo cells. Morphogenesis then organizes the bone cells into bone tissue to form bones and the muscle cells into muscle tissue to form muscles. However, it is the process of pattern formation that organizes those bones and muscles into the specific spatial organization that makes a dog look like a dog and a human look like a human.

    The Role of Positional Cues in Pattern Formation. During pattern formation, it is crucial for cells of the developing embryo to communicate with one another so that each cell will "know" its relative position within the emerging body plan. The intercellular molecular signals that ultimately drive the process of pattern formation provide positional information. These signals may be chemicals released by certain embryonic cells that diffuse through the embryo and bind to other cells. These diffusible signals are called morphogens. Oftentimes it is the concentration of the morphogen the target cell senses that provides information about the target cell's proximity to the releasing cell.

    The development of a chicken wing is a good example of this phenomenon. During development, the chick wing develops from a structure called the limb bud. Lewis Wolpert discovered a small collection of cells that lie along the rear margin of the limb bud and that specify the position of cells along the front-rear axis of the bud. Ultimately, these cells control the pattern of digit development in the wing (chicken digits are like human fingers). Wolpert named these cells the polarizing region. They release a morphogen that diffuses through the limb bud. The cells that are exposed to the highest concentration of morphogen (the ones closest to the polarizing region) develop into a particular digit, the cells that are exposed to an intermediate concentration of morphogen develop into a differently shaped digit, etc. Ultimately the positional cue directs differentiation of the target cell by changing its pattern of gene expression.

    The Role of Hox Genes in Pattern Formation. The basic three-dimensional layout of an organism is established early in embryonic development. Even an early embryo body has dorsal and ventral axes (top and bottom) as well as anterior and posterior axes (front and back). The differential expression of certain genes in different cells of the embryo controls the emergence of this organization. Interestingly, while different types of organisms have dramatically different morphological features, a similar family of genes controls differential gene expression during pattern formation. The Hox family of genes (also called homeotic genes) is found in many different organisms (including plants and animals), and is important in controlling the anatomical identity of different parts of a body along its anterior/posterior axis. Many species have genes that include a nearly identical DNA sequence, called the homeobox region. These genes comprise the Hox family of genes, and they encode proteins that function as transcription factors. In fruit flies, for example, homeotic genes specify the types of appendages that develop on each body segment. The homeotic genes antennal and leg development by regulating the expression of a variety of other genes. The importance of the Hox genes is vividly evident when one of these genes is mutated: the wrong body part forms. For example, mutation in the Antennapedia gene causes fruit flies to develop legs in place of antennae on the head segment.


    How Autophagy Takes Place in a Cell

    The process of autophagy is initiated in response to molecular triggers that indicate damage, starvation, oxidative stress, or pathogenic invasion. The components to be recycled are marked and targeted for degradation by lysosomes. These are small spherical organelles that comprise an acidic interior containing a set of digestive enzymes.

    Depending on the precise pathway followed to introduce the targeted components into the lysosomes, autophagy has been classified as macroautophagy, microautophagy, and chaperone-mediated autophagy. Each of these have been explained below.

    Macroautophagy

    This is the main pathway for autophagy, and hence, the word ‘autophagy’ is often used synonymously with ‘macroautophagy.’ It involves bulk degradation of organelles and proteins that are introduced into the lysosome through specialized vesicles.

    The conditions of starvation are sensed by a protein called TOR (target of rapamycin), which is responsible for regulating the metabolism and protein synthesis inside the cell. In the absence of nutrients, growth factors, or oxygen, the activity of TOR is inhibited, which leads to the induction of macroautophagy in the cell.

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    In response to such induction, a double-layered membrane called phagophore or isolation membrane begins to form in the cytosol. Several proteins and lipid molecules participate in the formation of phagophore, at the right site of the cytosol and around the right cellular components.

    This membrane further elongates to surround the cargo targeted for degradation, which generally includes some part of the cytosol, certain long-lived or damaged proteins, and old or damaged organelles. The extreme ends of the membrane fuse together to form a double-membrane vesicle, which is termed autophagosome.

    Once the autophagosome is formed, the proteins that participated in building the membrane are released into the cytosol. These proteins are then free to assist the formation of new phagophores, whenever required.

    The function of this auophagosome is to fuse with, and deliver the cargo into the lysosomes. The outer layer of the autophagosome membrane fuses with the lysosomal membrane, thus, releasing a single-layered vesicle into the lysosome. The digestive enzymes present in the lysosomes degrade the single-layered membrane, and the lysosome is now termed as autolysosome.

    The inner cargo is now exposed to the lytic enzymes, like proteases, lipases, and hydrolases. These enzymes break down the cargo into basic building blocks, like amino acids, sugars, other carbohydrate moieties, as well as certain lipid molecules. These are then released into the cytosol for building new molecules, and they are used as an energy source to fuel metabolic processes of the cells.

    Microautophagy

    This mechanism of autophagy involves the direct entry of targeted cellular components into the lysosomes. Cytosolic molecules, like glycogen, protein aggregates, misfolded proteins, and organelles may be degraded through microautophagy.

    The process begins with the formation of tubular invagination of the lysosome. The lysosomal membrane forms tube-like projections that surround the targeted molecule or organelle.

    The surrounding membrane projections fuse together to form an intralysosomal vesicle that contains the cargo. The lytic enzymes can now degrade this cargo, and the building blocks are released into the cytosol.

    A special case of microautophagy is micronucleophagy or piecemeal microautophagy of the nucleus, during which a part of the nucleus is sequestered and degraded.

    Chaperone-mediated Autophagy (CMA)

    This route of autophagy functions to degrade only a specific set of misfolded, or erroneously formed cytosolic proteins. The proteins are identified and guided into the lysosome through cytosolic molecular assistants called chaperones.

    The proteins to be degraded through the CMA contain a unique motif that is biochemically related to the pentapeptide KFERQ. When the protein is not correctly folded, or is damaged, this motif gets exposed and is recognized by a molecular chaperone called hsc70 (heat shock cognate protein of 70KDa). Hsc70 binds to this unique motif and guides the protein, or CMA substrate, to the lysosomal surface.

    The lysosomal surface has a protein called lysosome-associated membrane protein type 2A (LAMP-2A), embedded into its membrane. This protein serves as a receptor for the substrate-hsc70 complex.

    Once the substrate-hsc70 complex binds to the LAMP-2A monomer, hsc70 as well as other membrane molecules and chaperones, like hsp90 (heat shock protein 90) unfold the substrate protein. Also, the LAMP-2A protein undergoes conformational changes and multimerization to form a hollow, cylindrical transport structure called CMA translocation complex.

    The unfolded substrate passes through the translocation complex and enters the lysosomal lumen. A variant of the hsc70, called lysosomal hsc70, is present in the lumen of the lysosome. It helps in pulling the substrate inside the lysosome, and it also prevents it from returning to the cytosol.

    Once the substrate passes into the lysosomal lumen, the CMA translocation complex is immediately disassembled by hsc70, hsp 90, and other proteins present at the lysosomal membrane. The substrate is degraded by proteases present in the lumen, and the resultant amino acids are released into the cytosol.

    Autophagy and Cell Death

    Autophagy is known to be a cell survival mechanism, and has been shown to inhibit programmed cell death or apoptosis (a form of cellular suicide). However, certain experiments have demonstrated the induction of cell death by macroautophagy, thereby, suggesting it to be one of the mechanisms through which cells commit suicide. It is characterized by bulk degradation of key proteins or organelles that are essential for survival of the cell and an accumulation of several autophagosomes inside the cell. Such cell death is termed as autophagic cell death (ACD). However, the precise mechanisms that lead to ACD as well as the connection between autophagy and apoptosis is not yet clear.

    Autophagy plays a vital role in several physiological processes, like tissue repair, maintaining cellular and tissue homeostasis, as well as aging. Alterations in autophagic pathways have been associated with several muscular and neurodegenerative disorders, deterioration of heart muscles, as well as certain types of cancers. Its precise role in cell survival and cell death is being explored extensively.

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    Mitochondria

    Mitochondria (singular- mitochondrion) are the energy powerhouses of cells. Much of the energy that cells (and therefore individuals) require to function is harvested from biomolecules such as sugars and fats obtained from food. Mitochondria carry out the final steps of converting the food to energy. Like the nucleus, mitochondria are surrounded by a double membrane.

    Like the burning of gasoline in an automobile engine, the energy production process is not completely efficient and produces by-products that often have undesirable effects. Energy production in mitochondria leads to the production of chemicals that may damage DNA and therefore cause genetic changes. These dangerous side products are thought to contribute to the mutations seen in cancer cells.

    A diagram of a mitochondrion, showing the two separate membranes and the inner compartment that is the site of energy production is shown below.

    In the image below, the mitochondria in mouse cells have been stained red. The nuclei and chromosomes of the cells are blue. Note the wide distribution, large number and the somewhat irregular shapes of the mitochondria. The green regions near the nucleus in each cell are organelles known as the golgi apparatus, they are involved in the modification and shipment of biomolecules such as proteins.

    The image above was used with the permission of the copyright owner, Molecular Probes.


    Scientists Create Simple Synthetic Cell That Grows and Divides Normally

    Five years ago, scientists created a single-celled synthetic organism that, with only 473 genes, was the simplest living cell ever known. However, this bacteria-like organism behaved strangely when growing and dividing, producing cells with wildly different shapes and sizes.

    Now, scientists have identified seven genes that can be added to tame the cells’ unruly nature, causing them to neatly divide into uniform orbs. This achievement, a collaboration between the J. Craig Venter Institute (JCVI), the National Institute of Standards and Technology (NIST) and the Massachusetts Institute of Technology (MIT) Center for Bits and Atoms, is described in the journal Cell.

    Identifying these genes is an important step toward engineering synthetic cells that do useful things. Such cells could act as small factories that produce drugs, foods and fuels detect disease and produce drugs to treat it while living inside the body and function as tiny computers.

    But to design and build a cell that does exactly what you want it to do, it helps to have a list of essential parts and know how they fit together.

    “We want to understand the fundamental design rules of life,” said Elizabeth Strychalski, a co-author on the study and leader of NIST’s Cellular Engineering Group. “If this cell can help us to discover and understand those rules, then we’re off to the races.”

    Scientists at JCVI constructed the first cell with a synthetic genome in 2010. They didn’t build that cell completely from scratch. Instead, they started with cells from a very simple type of bacteria called a mycoplasma. They destroyed the DNA in those cells and replaced it with DNA that was designed on a computer and synthesized in a lab. This was the first organism in the history of life on Earth to have an entirely synthetic genome. They called it JCVI-syn1.0.

    Since then, scientists have been working to strip that organism down to its minimum genetic components. The super-simple cell they created five years ago, dubbed JCVI-syn3.0, was perhaps too minimalist. The researchers have now added 19 genes back to this cell, including the seven needed for normal cell division, to create the new variant, JCVI-syn3A. This variant has fewer than 500 genes. To put that number in perspective, the E. coli bacteria that live in your gut have about 4,000 genes. A human cell has around 30,000.

    “We want to understand the fundamental design rules of life. If this cell can help us to discover and understand those rules, then we’re off to the races.” —Elizabeth Strychalski, a co-author on the study and leader of NIST’s Cellular Engineering Group

    Identifying those seven additional genes took years of painstaking effort by JCVI’s synthetic biology group, led by co-author John Glass. Co-lead author and JCVI scientist Lijie Sun constructed dozens of variant strains by systematically adding and removing genes. She and the other researchers would then observe how those genetic changes affected cell growth and division.

    NIST’s role was to measure the resulting changes under a microscope. This was a challenge because the cells had to be alive for observation. Using powerful microscopes to observe dead cells is relatively easy. Imaging live cells is much harder.

    Holding these cells in place under a microscope was particularly difficult because they are so small and delicate. A hundred or more would fit inside a single E. coli bacterium. Tiny forces can tear them apart.

    To solve this problem, Strychalski and MIT co-authors James Pelletier, Andreas Mershin and Neil Gershenfeld designed a microfluidic chemostat — a sort of mini-aquarium — where the cells could be kept fed and happy under a light microscope. The result was stop-motion video that showed the synthetic cells growing and dividing.

    This video shows JCVI-syn3.0 cells — the ones created five years ago — dividing into different shapes and sizes. Some of the cells form filaments. Others appear to not fully separate and line up like beads on a string. Despite the variety, all these cells are genetically identical.

    This video shows the new JCVI-Syn3A cells dividing into cells of more uniform shape and size.

    These videos and others like them allowed the researchers to observe how their genetic manipulations affected the cell growth and division. If removing a gene disrupted the normal process, they’d put it back and try another.

    “Our goal is to know the function of every gene so we can develop a complete model of how a cell works,” Pelletier said.

    But that goal has not been reached yet. Of the seven genes added to this organism for normal cell division, scientists know what only two of them do. The roles that the other five play in cell division are not yet known.

    “Life is still a black box,” Strychalski said. But with this simplified synthetic cell, scientists are getting a good look at what’s going on inside.