Cell biology Handout

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Cell biology Handout

Sources : - www.biologydaily.com www.biology.arizona.eduCell biology (also called cellular biology or cytology) is an academic discipline which studies the physiological properties of cells, as well as their behaviours, interactions, and environment; this is done both on a microscopic and molecular level. Cell biology researches both single-celled organisms like bacteria and specialized cells in multicellular organisms like humans. Understanding the composition of cells and how cells works is fundamental to all of the biological sciences. Appreciating the similarities and differences between cell types is particularly important to the fields of cell and molecular biology. These fundamental similarities and differences provide a unifying theme, allowing the principles learned from studying one cell type to be extrapolated and generalized to other cell types. Research in cell biology is closely related to genetics, biochemistry, molecular biology and developmental biology.

Purification of cells and their parts Purification of cells and their parts is achieved in the following ways: Cell fractionation

Flow cytometry

Release of cellular organelles by disruption of cells.

Separation of different organelles by centrifugation.

Proteins extracted from membranes by detergents and salts.

The cell is the structural and functional unit of all living organisms. Some organisms, such as bacteria, are unicellular, consisting of a single cell. Other organisms, such as humans, are multicellular, (humans have an estimated 100,000 billion = 1014 cells). The cell theory, first developed in the 19th century, states that all organisms are composed of one or more cells; all cells come from preexisting cells; all vital functions of an organism occur within cells and that cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells.

The word cell comes from the Latin cella, a small room. The name was chosen by Robert Hooke because of the likeness he saw between cork cells and small rooms.

Each cell is a self-contained and self-maintaining entity: it can take in nutrients, convert these nutrients into energy, carry out specialized functions, and reproduce as necessary. Each cell stores its own set of instructions for carrying out each of these activities.

All cells share several abilities:

Reproduction by cell division.

Metabolism, including taking in raw materials, building cell components, creating energy molecules and releasing by-products. The functioning of a cell depends upon its ability to extract and use chemical energy stored in organic molecules. This energy is derived from metabolic pathways.

Synthesis of proteins, the functional workhorses of cells, such as enzymes. A typical mammalian cell contains up to 10,000 different proteins.

Response to external and internal stimuli such as changes in temperature, pH or nutrient levels.

Traffic of vesicles.

Types of cells

One way to classify cells is whether they live alone or in groups. Organisms vary from single cells (called single-celled or unicellular organisms) that function and survive more or less independently, through colonial forms with cells living together, to multicellular forms in which cells are specialized and do not generally survive once separated. 220 types of cells and tissues make up the multicellular human body.

Cells can also be classified into two categories based on their internal structure.

Prokaryotic cells are structurally simple. They are found only in single-celled and colonial organisms. In the three-domain system of scientific classification, prokaryotic cells are placed in the domains Archaea and Eubacteria.

Eukaryotic cells have organelles with their own membranes. Single-celled eukaryotic organisms are very diverse, but many colonial and multicellular forms also exist. (The multicellular kingdoms, i.e., Animalia, Plantae and Fungi, are all eukaryotic.)

Components of cells

Schematic of typical animal cell. Organelles: (1) nucleolus (2) nucleus (3) ribosome (4) vesicle,(5) rough endoplasmic reticulum (ER), (6) Golgi apparatus, (7) Cytoskeleton, (8) smooth ER, (9) mitochondria, (10) vacuole, (11) cytoplasm, (12) lysosome, (13) centriolesAll cells whether prokaryotic or eukaryotic have a membrane, which envelopes the cell, separates its interior from the surroundings, strictly controls what moves in and out and maintains the electric potential of the cell. Inside the membrane is a salty cytoplasm (the substance which makes up most of the cell volume). All cells possess DNA, the hereditary material of genes and RNA, which contain the information necessary to express various proteins such as enzyme, the cell's primary machinery. Within the cell at any given time are various additional biomolecules. This article will briefly overview these primary components of the cell then continue to briefly describe their function.

Cell membrane - a cell's protective coat

The outer lining of a eukaryotic cell is called the plasma membrane. A form of plasma membrane is also found in prokaryotes, but in this organism it is usually referred to as the cell membrane. This membrane serves to separate and protect a cell from its surrounding environment and is made mostly from a double layer of lipids (fat-like molecules) and proteins. Embedded within this membrane are a variety of other molecules that act as channels and pumps, moving different molecules into and out of the cell.

Cytoskeleton - a cell's scaffold

The cytoskeleton is an important, complex, and dynamic cell component. It acts to organize and maintain the cell's shape; anchors organelles in place; helps during endocytosis, the uptake of external materials by a cell; and moves parts of the cell in processes of growth and motility. There are a great number of proteins associated with the cytoskeleton, each controlling a cells structure by directing, bundling, and aligning filaments.

Cytoplasm - a cell's inner space

Inside the cell there is a large fluid-filled space called the cytoplasm. This refers both to the mixture of ions and fluids in solution within the cell, and the organelles contained in it which are separated from this intercellular "soup" by their own membranes. The cytosol refers only to the fluid, and not to the organelles.

In prokaryotes, the cytoplasm is relatively free of compartments. In eukaryotes, it normally contains a large number of organelles, and is the home of the cytoskeleton. The cytosol contains dissolved nutrients, helps break down waste products, and moves material around the cell through a process called cytoplasmic streaming. The nucleus often flows with the cytoplasm changing its shape as it moves. The cytoplasm also contains many salts and is an excellent conductor of electricity, creating the perfect environment for the mechanics of the cell. The function of the cytoplasm, and the organelles which reside in it, are critical for a cell's survival.

Genetic material

Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Most organisms use DNA for their long term information storage, but a few viruses have RNA as their genetic material. The biological information contained in an organism is encoded in its DNA or RNA sequence. Note that RNA is also used for information transport (mRNA) and enzymatic functions (like ribosomal RNA) in most organisms.

Prokaryotic genetic material is organized in a simple circular DNA molecule (the bacterial chromosome) that rests in the cytoplasm (more specifically in the nucleoid region). Eukaryotic genetic material is more complex (DNA is condensed with proteins) and is divided into different, linear molecules called chromosomes, which are found inside the nucleus and can come in an haploid or diploid set. Besides some organelles have their own genetic material, which is complemented by the nuclear genome (see endosymbiotic theory).

Human genetic material, for example, is made up of two distinct components: the nuclear genome and the mitochondrial genome. The nuclear genome (being diploid) is divided into 46 linear DNA molecules, each contained in a different chromosome. The mitochondrial genome is a circular DNA molecule separate from the nuclear DNA. Although the mitochondrial genome is very small, it codes for some very important proteins.

Organelles

The human body contains many different organs, such as the heart, lung, and kidney, with each organ performing a different function. Cells also have a set of "little organs", called organelles, that are adapted and/or specialized for carrying out one or more vital functions. Organelles are found only in eukaryotes and are, with a few exceptions, surrounded by a protective membrane.

Cell nucleus - a cell's center: The cell nucleus is the most conspicuous organelle found in a eukaryotic cell. It houses the cell's chromosomes and is the place where almost all DNA replication and RNA synthesis occur. The nucleus is spheroid in shape and separated from the cytoplasm by a double membrane called the nuclear envelope. The nuclear envelope isolates and protects a cell's DNA from various molecules that could accidentally damage its structure or interfere with its processing. During processing, DNA is transcribed, or copied into a special RNA, called mRNA. This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. In prokaryotes, DNA processing takes place in the cytoplasm.

Ribosomes - the protein production machine: Ribosomes are found in both prokaryotes and eukaryotes. The ribosome is a large complex composed of many molecules, including RNAs and proteins, and is responsible for processing the genetic instructions carried by an mRNA. The process of converting an mRNA's genetic code into the exact sequence of amino acids that make up a protein is called translation. Protein synthesis is extremely important to all cells, and therefore a large number of ribosomessometimes hundreds or even thousandscan be found throughout a cell.

Mitochondria and chloroplasts - the power generators: Mitochondria are self-replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. As mentioned earlier, mitochondria contain their own genome that is separate and distinct from the nuclear genome of a cell. Mitochondria play a critical role in generating energy in the eukaryotic cell, and this process involves a number of complex metabolic pathways.

Endoplasmic reticulum and Golgi apparatus - macromolecule managers:: The endoplasmic reticulum (ER) is the transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that will float freely in the cytoplasm. The ER has two forms: the rough ER and the smooth ER. The rough ER is labeled as such because it has ribosomes adhering to its outer surface, whereas the smooth ER does not. Translation of the mRNA for those proteins that will either stay in the ER or be exported (moved out of the cell) occurs at the ribosomes attached to the rough ER. Proteins to be exported are passed to the Golgi apparatus, sometimes called a Golgi body or Golgi complex, for further processing, packaging, and transport to a variety of other cellular locations. The smooth ER serves for lipids synthesis, detoxification and as a calcium reservoir.

Lysosomes and peroxisomes - the cellular digestive system: Lysosomes and peroxisomes are often referred to as the garbage disposal system of a cell. Both organelles are somewhat spherical, bound by a single membrane, and rich in digestive enzymes, naturally occurring proteins that speed up biochemical processes. For example, lysosomes can contain more than three dozen enzymes for degrading proteins, nucleic acids, and certain sugars called polysaccharides. Here we can see the importance behind compartmentalization of the eukaryotic cell. The cell could not house such destructive enzymes if they were not contained in a membrane-bound system.

Anatomy of cells

Eukaryotic cells are about 10 times the size of a prokaryote and can be as much as 1000 times greater in volume. The major and extremely significant difference between prokaryotes and eukaryotes is that eukaryotic cells contain membrane-bound compartments in which specific metabolic activities take place. Most important among these is the presence of a nucleus, a membrane-delineated compartment that houses the eukaryotic cells DNA. It is this nucleus that gives the eukaryoteliterally, true nucleusits name. Eukaryotic organisms also have other specialized structures, performing dedicated functions, the aforementioned organelles. Other differences include:

The cytoplasm of eukaryotes does not appear as granular as that of prokaryotes, since an important part of the ribosomes are bound to the endoplasmic reticulum.

The plasma membrane resembles that of prokaryotes in function, with minor differences in the setup. Cell walls may or may not be present.

The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are highly condensed (e.g. folded around histones). All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. Some eukaryotic organelles can contain some DNA.

Eukaryotes can become mobile using cilia or flagella. The flagella are more complex than those of prokaryotes.

Table 1: Comparison of features of prokaroytic and eukaryotic cells

Prokaryotes Eukaryotes

Typical organisms bacteria, archaea protists, fungi, plants, animals

Typical size ~ 1-10 m ~ 10-100 m (sperm cells, apart from the tail, are smaller)

Type of nucleus nucleoid region; no real nucleus real nucleus with double membrane

DNA circular (usually) linear molecules (chromosomes) with histone proteins

RNA-/protein-synthesis coupled in cytoplasm RNA-synthesis inside the nucleusprotein synthesis in cytoplasm

Ribosomes 50S+30S 60S+40S

Cytoplasmatic structure very few structures highly structured by endomembranes and a cytoskeleton

Cell movement flagella made of flagellin flagella and cilia made of tubulin

Mitochondria none one to several dozen (though some lack mitochondria)

Chloroplasts none in algae and plants

Organization Usually single cells single cells, colonies, higher multicellular organisms with specialized cells

Cell division Binary fission (simple division) Mitosis Meiosis

Cell functions

Cell growth and metabolism

Between successive cell divisions cells grow through the functioning of cellular metabolism. Cell metabolism is the process by which individual cells process nutrient molecules. Metabolism has two distinct divisions; catabolism, in which the cell breaks down complex molecules to produce energy and reducing power, and anabolism, where the cell uses energy and reducing power to construct complex molecules and perform other biological functions. Complex sugars consumed by the organism can be broken down into a less chemically complex sugar molecule called glucose. Once inside the cell, glucose is broken down to make adenosine triphosphate (ATP), a form of energy, via two different pathways.

The first pathway, glycolysis, requires no oxygen and is referred to as anaerobic metabolism. Each reaction is designed to produce some hydrogen ions that can then be used to make energy packets (ATP). In prokaryotes, glycolysis is the only method used for converting energy. The second pathway, called the Kreb's cycle, or citric acid cycle, occurs inside the mitochondria and is capable of generating enough ATP to run all the cell functions.

Making new cells

Cell division involves a single cell (called a mother cell) dividing into two daughter cells. This leads to growth in multicellular organisms (the growth of tissue) and to procreation (vegetative reproduction) in unicellular organisms. Eukaryotic cells usually undergo a process of nuclear division, called mitosis, followed by division of the cell, called cytokinesis. A diploid cell may also undergo meiosis to produce haploid cells, usually four. Haploid cells serve as gametes in multicellular organisms, fusing to form new diploid cells. DNA replication, or the process of duplicating a cell's genome, is required every time a cell divides. Replication, like all cellular activities, requires specialized proteins for carrying out the job.

Protein synthesis

Protein synthesis is the process in which the cell builds proteins. DNA transcription refers to the synthesis of a messenger RNA (mRNA) molecule from a DNA template. This process is very similar to DNA replication. Once the mRNA has been generated, a new protein molecule is synthesized via the process of translation.

The cellular machinery responsible for synthesizing proteins is the ribosome. The ribosome consists of structural RNA and about 80 different proteins. When the ribosome encounters an mRNA, the process of translating an mRNA to a protein begins. The ribosome accepts a new transfer RNA, or tRNAthe adaptor molecule that acts as a translator between mRNA and proteinbearing an amino acid, the building block of the protein. Another site binds the tRNA that becomes attached to the growing chain of amino acids, forming the a polypeptide chain that will eventually be processed to become a protein.

Origins of cells

The origin of cells has to do with the origin of life, and was one of the most important steps in evolution of life as we know it. The birth of the cell marked the passage from prebiotic chemistry to biological life. If life is viewed from the point of view of replicators, that is DNA molecules in the organism, cells satisfy two fundamental conditions: protection from the outside environment and confinement of biochemical activity. The former condition is needed to maintain the fragile DNA chains stable in a varying and sometimes aggressive environment, and may have been the main reason for which cells evolved. The latter is fundamental for the evolution of biological complexity . If freely-floating DNA molecules that code for enzymes that are not enclosed into cells, the enzymes that advantage a given DNA molecule (for example, by producing nucleotides) will automatically advantage the neighbouring DNA molecules. This might be viewed as "parasitism by default". Therefore the selection pressure on DNA molecules will be much lower, since there is not a definitive advantage for the "lucky" DNA molecule that produces the better enzyme over the others: all molecules in a given neighbourhood are almost equally advantaged. If all the DNA molecule is enclosed in a cell, then the enzymes coded from the molecule will be kept close to the DNA molecule itself. The DNA molecule will directly enjoy the benefits of the enzymes it codes, and not of others. This means other DNA molecules won't benefit from a positive mutation in a neighbouring molecule: this means that positive mutations give immediate and selective advantage to the replicator bearing it, and not on others. This is thought to have been the one of the main driving force of evolution of life as we know it. (Note. This is more a metaphor given for simplicity than complete accuracy, since the earliest molecules of life, probably up to the stage of cellular life, were most likely RNA molecules, acting both as replicators and enzymes: see RNA world hypothesis . But the core of the reasoning is the same.)

Biochemically, cell-like spheroids formed by proteinoids are observed by heating amino acids with phosphoric acid as a catalyst. They bear much of the basic features provided by cell membranes. Proteinoid-based protocells enclosing RNA molecules could (but not necessarily should) have been the first cellular life forms on Earth.

Origin of eukaryotic cells

The eukaryotic cell seems to have evolved from a symbiotic community of prokaryotic cells. It is almost certain that DNA-bearing organelles like the mitochondria and the chloroplasts are what remains of ancient symbiotic oxygen-breathing bacteria and cyanobacteria, respectively, where the rest of the cell seems to be derived from an ancestral archaean prokaryote cell a theory termed the endosymbiotic theory.

There is still considerable debate on if organelles like the hydrogenosome predated the origin of mitochondria, or viceversa: see the hydrogen hypothesis for the origin of eukaryotic cells.

History

1632-1723: Antony van Leeuwenhoek teaches himself to grind lenses, builds a microscope and draws protozoa, such as Vorticella from rain water, and bacteria from his own mouth.

1665: Robert Hooke discovers cells in cork, then in living plant tissue using an early microscope.

...I could exceedingly plainly perceive it to be all perforated and porous, much like a Honeycomb...these pores or cells, were not very deep, but consisted of a great many little boxes... Hooke describing his observations on a thin slice of cork.

1839: Theodor Schwann and Matthias Jakob Schleiden elucidate the principal that plants and animals are made of cells, concluding that cells are a common unit of structure and development, thus founding the Cell Theory.

The belief that life forms are able to occur spontaneously (generatio spontanea) is contradicted by Louis Pasteur (1822-1895).

Rudolph Virchow states that cells always emerge from cell divisions (omnis cellula ex cellula).

1931: Ernst Ruska builds first transmission electron microscope (TEM) at the University of Berlin. By 1935 he has built an EM with twice the resolution of a light microscope, revealing previously unresolvable organelles.

1953: Watson and Crick made their first announcement on the double-helix structure for DNA on February 28.

1981: Lynn Margulis published Symbiosis in Cell Evolution detailing the endosymbiotic theory.

Cell membrane

The selectively permeable cell membrane (or plasma membrane or plasmalemma) is a thin and structured bilayer of phospholipid and protein molecules that envelopes the cell. It separates a cell's interior from its surroundings and controls what moves in and out. Cell surface membranes often contain receptor proteins and cell adhesion proteins. There are also other proteins with a variety of functions. These membrane proteins are important for the regulation of cell behavior and the organization of cells in tissues.

Transmembrane receptorTransmembrane receptors are integral membrane proteins, which reside and operate typically within a cell's plasma membrane, but also in the membranes of some subcellular compartments and organelles. Binding to a signalling molecule or sometimes to a pair of such molecules on one side of the membrane, transmembrane receptors initiate a response on the other side. In this way they play a unique and important role in cellular communications and signal transduction.

Many transmembrane receptors are composed of two or more protein subunits which operate collectively and may dissociate when ligands bind, fall off, or at another stage of their "activation" cycles. They are often classified based on their molecular structure, or because the structure is unknown in any detail for all but a few receptors, based on their hypothesized (and sometimes experimentally verified) membrane topology. The polypeptide chains of the simplest are predicted to cross the lipid bilayer only once, while others cross as many as seven times (the so-called G-protein coupled receptors).

Like any integral membrane protein, a transmembrane receptor may be subdivided into three parts or domains.

E=extracellular space; I=intracellular space; P=plasma membrane

The extracellular domain

The extracellular domain is the part of the receptor that sticks out of the membrane on the outside of the cell or organelle. If the polypeptide chain of the receptor crosses the bilayer several times, the external domain can comprise several "loops" sticking out of the membrane. By definition. a receptor's main function is to recognize and respond to a specific ligand, for example, a neurotransmitter or hormone (although certain receptors respond also to changes in transmembrane potential), and in many receptors these ligands bind to the extracellular domain.

The transmembrane domain

In the majority of receptors for which structural evidence exists, transmembrane alpha helices make up most of the transmembrane domain. In certain receptors, such as the nicotinic acetylcholine receptor, the transmembrane domain forms a protein-lined pore through the membrane, or ion channel. Upon activation of an extracellular domain by binding of the appropriate ligand, the pore becomes accessible to ions, which then pass through. In other receptors, the transmembrane domains are presumed to undergo a conformational change upon binding, which exerts an effect intracellularly. In some receptors, such as members of the 7TM superfamily, the transmembrane domain may contain the ligand binding pocket (evidence for this and for much of what else is known about this class of receptors is based in part on studies of bacteriorhodopsin, the detailed structure of which has been determined by crystallography).

The intracellular domain

The intracellular (or cytoplasmic) domain of the receptor interacts with the interior of the cell or organelle, relaying the signal. There are two fundamentally different ways for this interaction:

The intracellular domain communicates via specific protein-protein-interactions with effector proteins, which in turn send the signal along a signal chain to its destination.

The intracellular domain has enzymatic activity. Often, this is a tyrosine kinase activity. The enzymatic activity can also be located on an enzyme associated with the intracellular domain.

Regulation of receptor activity

There are several ways for the cell to regulate the activity of a transmembrane receptor. Most of them work through the intracellular domain. The most important ways are phosphorylation and internalization (see ubiquitin).

Phosphorylation is the addition of a phosphate (PO4) group to a protein or a small molecule. Its prominent role in biochemistry is the subject of a very large body of research (the Medline database returns over 100,000 articles on the subject, largely on protein phosphorylation).

Protein phosphorylation

Function

Protein phosphorylation is probably the most important regulatory event. Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation. Phosphorylation is catalyzed by various specific protein kinases, whereas phosphatases dephosphorylate.

An example of the important role that phosphorylation plays is the p53 tumor suppressor gene, whichwhen activestimulates transcription of gene that suppress the cell cycle, even to the extent that it undergoes apoptosis. However, this activity should be limited to situations where the cell is damaged or physiology is disturbed. To this end, the p53 protein is extensively regulated. In fact, p53 contains more than 18 different phosphorylation sites.

Upon the deactivating signal, the protein becomes dephosphorylated again and stops working. This is the mechanism in many forms of signal transduction, for example the way in which incoming light is processed in the light-sensitive cells of the retina.

Signaling networks

The network underlying phosphorylation can be very complex. In some cellular signalling pathways, a protein A phosphorylates B, and B phosphorylates C, but A also phosphorylates C directly, and B can phosphorylate D, which may in turn phosphorylate A.

Types of phosphorylation

Within a protein, phosphorylation can occur on several amino acids. Phosphorylation on serine is the most common, followed by threonine. Tyrosine phosphorylation is relatively rare. However, since tyrosine phosphorylated proteins are relatively easy to purify using antibodies, tyrosine phosphorylation sites are relatively well understood.

A protein kinase is an enzyme that can transfer a phosphate group from a donor molecule (usually ATP) to an amino acid residue of a protein. The protein kinase mechanism is used in signal transduction for the regulation of enzymes: phosphorylation can activate (or inhibit) the activity of an enzyme. Although most protein kinases are specialized for a single kind of amino acid residue, some exhibit dual kinase activity (they can phosphorylate two different kinds of amino acids).Other kinds ATP, the "high-energy" exchange medium in the cell, is synthesized in the mitochondrion by addition of a third phosphate group to ADP in a process referred to as oxidative phosphorylation. ATP is also synthesized by substrate level phosphorylation during glycolysis. Phosphorylation of sugars is often the stage of their catabolism. It allows cells to accumulate sugars because the phosphate group prevents the molecules from diffusing back across their transporter.

A tyrosine kinase is an enzyme that can transfer a phosphate group to a tyrosine residue in a protein; these enzymes are a subgroup of the larger class of protein kinases. Phosphorylation is an important function in signal transduction to regulate enzyme activity. The hormones that act on tyrosine kinase receptors are generally growth hormones and factors that promote cell division (e.g., insulin, insulin-like growth factor 1, epidermal-derived growth factor).

A Fluid Mosaic

The basic composition and structure of the plasma membrane is the same as that of the membranes that surround organelles and other subcellular compartments. The foundation is a phospholipid bilayer, and the membrane as a whole is often described as a 'fluid mosaic' - a two-dimensional fluid of freely diffusing lipids, dotted or embedded with proteins which may function as channels or transporters across the membrane, or as receptors. Some of these proteins simply adhere to the membrane (extrinsic or peripheral proteins), while others might be said to reside within it or to span it (intrinsic proteins -- more at integral membrane protein). Glycoproteins have carbohydrates attached to their extracellular domains. Cells may vary the variety and the relative amounts of different lipids to maintain the fluidity of their membranes despite changes in temperature. Cholesterol molecules (in case of eukaryotes) or hopanoids (in case of prokaryotes) in the bilayer assist in regulating fluidity.

Phospholipids are formed from four components: fatty acids, a negatively charged phosphate group, an alcohol and a backbone. Phospholipids with a glycerol backbone are known as phosphoglycerides. There is only one type of phospholipid with a sphingosine backbone; sphingomyelin. Phospholipids are a major component of all biological membranes, along with glycolipids and cholesterol.

Detailed Structure

In fact, not all lipid molecules in the cell membrane are "fluid," in the sense of free to diffuse. Lipid rafts and caveolae are examples of more cohesive membrane regions. Across the membrane globally, also many proteins are not entirely free to diffuse. The cytoskeleton undergirds the cell membrane and provides anchoring points for integral membrane proteins. Anchoring restricts them to a particular cell face or surface--for example, the "apical" surface of epithelial cells that line the vertebrate gut--and limits how far they may diffuse within the bilayer. Finally, rather than presenting always a formless and fluid contour, the plasma membrane surface of cells may show structure. Returning to the example of epithelial cells in the gut, the apical surfaces of many such cells are dense with involutions, all similar in size. The finger-like projections, called "microvilli", increase cell surface area and facilitate the absorption of molecules from the outside. Synapses are another example of highly structured membrane.

Transport across membranes

As a lipid bilayer, the cell membrane is selectively permeable. This means that only some molecules can pass unhindered in or out of the cell. These molecules are either small or lipophilic. Other molecules can pass in or out of the cell, if there are specific transport molecules.

Depending on the molecule, transport occurs by different mechanisms, which can be separated into those that do not consume energy in the form of ATP (passive transport) and those that do (active transport):

Passive transport

Passive transport is a means of moving biochemicals, and other atomic or molecular substances, across membranes. Unlike active transport, this process does not involve chemical energy (ATP). Passive transport is dependent on the permeability of the cell membrane, which, in turn, is dependent on the organization and characteristics of the membrane lipids and proteins. The four main kind of passive transport are diffusion, facilitated diffusion, filtration and osmosis.

Diffusion

Diffusion is the net movement of material from an area of high concentration of that material to an area with lower concentration. The difference of concentration between the two areas is often termed as the concentration gradient, and diffusion will continue until this gradient has been eliminated. Since diffusion moves material from area of higher concentration to the lower, it is described as moving solutes "down the concentration gradient" (compared with active transport, which often moves material from area of low concentration to area of higher concentration, and therefore referred to as moving the material "against the concentration gradient").

If and when the concentration gradient have been eliminated, no net exchange of material occurs. Although material may move forth from one area to the other, it will be balanced by movement of the same amount of material to the opposite direction.

Diffusion is biologically important because it enables the abolishment of concentration gradients in the body. For example, metabolic activity will consume oxygen, which will reduce its concentration in the bloodstream; diffusion of oxygen in the alveoli of the lungs allows it to be replenished.

Facilitated diffusion

Facilitated diffusion is movement of molecules across the cell membrane via special carrier proteins that are embedded within the cellular membrane. A lot of large molecules, such as glucose, are insoluble in lipids and too large to fit through the membrane pores. Therefore, it will bind with its specific carrier proteins, and the complex will then be bonded to a receptor site and moved through the cellular membrane. Bear in mind, however, that facilitated diffusion is a passive process, and the solutes still move down the concentration gradient.

Filtration

Filtration is movement of water and solute molecules across the cell membrane due to hydrostatic pressure generated by the cardiovascular system. Depending on the size of the membrane pores, only solutes of a certain size may pass through it. For example, the membrane pores of the Bowman's capsule in the kidneys are very small, and only albumin, the smallest of the proteins, have any chance of being filtered through. On the other hand, the membrane pores of liver cells are extremely large, to allow a veriety of solutes to pass through and be metabolized.

Osmosis

Osmosis is basically diffusion of water molecules. Most cell membranes are permeable to water, and since the diffusion of water plays such an important role in the biological functioning of any living being, a special term has been coined for it -- osmosis.

Water molecules "stick" together via weak hydrogen bonds; therefore, unlike most solutes, water molecules move around in large clumps, a phenomenon known as bulk flow.

Categories: Cell biology | Biochemistry | PhysiologyActive transport

Typically moves molecules against their electrochemical gradient , a process that would be entropically unfavorable were it not stoichiometrically coupled with the hydrolysis of ATP. This coupling can be either primary or secondary. In the primary active transport, transporters that move molecules against their electrical/chemical gradient, hydrolyze ATP. In the secondary active transport, transporters use energy derived from transport of another molecule in the direction of their gradient, to move other molecules in the direction against their gradient. This can be either symport (in the same direction) or antiport (in the opposite direction).

Examples include:

1. endocytosis

2. exocytosis, in which molecules packaged in membrane vesicles are either imported or exported, respectively. Molecular exchangers , transporters and pumps represent other examples.

Active transport is the mediated transport of biochemicals, and other atomic/molecular substances, across membranes. Unlike passive transport, this process requires chemical energy. In this form of transport, molecules move against either an electrical or concentration gradient (collectively termed an electrochemical gradient). This is achieved by either altering the affinity of the binding site or altering the rate at which the protein changes conformations.

Types

There are two main types, primary and secondary. In primary transport energy is directly coupled to movement of desired substance across a membrane, independent of any other species. Secondary transport concerns the diffusion of one species across a membrane to drive the transport of another.

Primary

Primary active transport directly uses energy to transport molecules across a membrane. Most of the enzymes that perform this type of transport are transmembrane ATPases. A primary ATPase universal to all cellular life is the sodium-potassium pump, which helps maintain the cell potential.

ATPases are a class of enzymes that catalyze the decomposition of adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and a free phosphate ion. This dephosphorylation reaction releases energy, which the enzyme (in most cases) harnesses to drive other chemical reactions that would not otherwise occur. Some such enzymes are integral membrane proteins (anchored within biological membranes), and move solutes across the membrane. (These are called transmembrane ATPases).

Transmembrane ATPases import many of the metabolites necessary for cell metabolism and export toxins, wastes, and solutes that can hinder cellular processes. An important example is the sodium-potassium exchanger (or Na+/K+ATPase), which establishes the ionic concentration balance that maintains the cell potential.

Secondary

In secondary active transport, there is no direct coupling of ATP; instead, the electrochemical potential difference created by pumping ions out of cells is used. The two main forms of this are counter-transport (antiport) and co-transport (symport).

Counter-transport

In counter-transport two species of ion or other solute are pumped in opposite directions across a membrane. One of these species is allowed to flow from high to low concentration, which yields the entropic energy to drive the transport of the other solute from a low concentration region to a high one. An example is the sodium-calcium exchanger or antiporter, which allows three sodium ions into the cell to transport one calcium out.

Many cells also posses a calcium ATPase, which can operate at lower intracellular concentrations of calcium and sets the normal or resting concentration of this important second messenger. But the ATPase exports calcium ions more slowly: only 30 per second versus 2000 per second by the exchanger. The exchanger comes into service when the calcium concentration rises steeply or "spikes" and enables rapid recovery. This shows that a single type of ion can be transported by several enzymes, which need not be active all the time (constitutively), but may exist to meet specific, intermittent needs.

Co-transport

Co-transport also uses the flow of one solute species from high to low concentration to move another molecule against its preferred direction of flow; but here, both solutes move in the same direction across the membrane. An example is the glucose symporter, which cotransports two sodiums for every molecule of glucose it imports into the cell.

Movement of proteins

Proteins are synthesized by ribosomes in the cytoplasm. This process is also known as protein biosynthesis or simply protein translation. Some proteins, such as those to be incorporated in membranes (membrane proteins), are transported into the ER during synthesis and further processed in the Golgi apparatus. From the Golgi, membrane proteins can move to the plasma membrane, to other subcellular comparments or they can be secreted from the cell. The ER and Golgi can be thought of as the "membrane protein synthesis compartment" and the "membrane protein processing compartment", respectively. There is a constant flux of proteins through these compartments. ER and Golgi-resident proteins associate with other proteins and remain in their respective compartments. Other proteins "flow" through the ER and Golgi to the plasma membrane. From the plasma membrane, proteins destined to be degraded move back into intracellular compartments where they are broken down to their individual amino acids.

Summary of the different methods by which molecules can enter cells.

Cell adhesion

Schematic of cell adhesion

Cells are often not found in isolation, rather they tend to stick to other cells or non-cellular components of their environment. A fundamental question is: what makes cells sticky? Cell adhesion generally involves protein molecules at the surface of cells, so the study of cell adhesion involves cell adhesion proteins and the molecules that they bind to.

Cell adhesion proteins (or Cell adhesion molecules, CAMs)

Cell adhesion proteins are often transmembrane receptors. Transmembrane cell adhesion proteins extend across the cell surface membrane and typically have domains that extend into both the extracellular space and the intracellular space. The extracellular domain of a cell adhesion protein can bind to other molecules that might be either on the surface of an adjacent cell (cell-to-cell adhesion) or part of the extracellular matrix (cell-to-ECM adhesion). The molecule that a cell adhesion protein binds to is called its ligand. There are families of cell adhesion proteins that can be characterized in terms of the structure of the adhesion proteins and their ligands. Adhesion between two copies of the same adhesion protein is called "homophilic" binding. Adhesion between an adhesion protein and some other molecule is "heterophilic" binding.

Major Cell Adhesion Protein Families

Familyligandsinteractions

Selectins Carbohydratesheterophilic

Integrins Extracellular matrixheterophilic

Ig superfamily proteinsheterophilic

Ig superfamily proteins Integrinsheterophilic

Ig superfamily proteinshomophilic

Cadherins Cadherinshomophilic

Cytoskeletal interactionsFor a cell adhesion protein like the one shown in the diagram, the intracellular domain binds to protein components of the cell's cytoskeleton. This allows for very tight adhesion. Without attachment to the cytoskeleton, a cell adhesion protein that is tightly bound to a ligand would be in danger of being ripped out of the fragile cell membrane. Often the connection between the cell adhesion proteins and the cytoskeleton is not as direct as shown in the diagram. For example, cadherin cell adhesion proteins are typically coupled to the cytoskeleton by way of special linking proteins called "catenins".

Importance of cell adhesionCell adhesion proteins are important for the normal functioning of living organisms. Cell adhesion proteins hold together the components of solid tissues. They are also important for the function of migratory cells like white blood cells. Regulation of cell adhesion proteins is important during embryonic development for the process of morphogenesis. Some people have "blistering diseases" that result from inherited molecular defects in genes for adhesion proteins. Some cancers involve mutations in genes for adhesion proteins that result in abnormal cell-to-cell interactions and tumor growth. Cell adhesion proteins are also important for interactions that allow viruses and bacteria to cause damage to humans. Cell adhesion proteins hold synapses together and the regulation of synaptic adhesion is involved in learning and memory. In Alzheimer's disease there is abnormal regulation of synaptic cell adhesion.

Desmosome

Cell adhesion in desmosomes

A desmosome (also known as macula adherens) is a cell structure specialized for cell-to-cell adhesion. Desmosomes are molecular complexes of cell adhesion proteins and linking proteins that attach the cell surface adhesion proteins to intracellular keratin cytoskeletal filaments. The cell adhesion proteins of the desmosome are members of the cadherin family of cell adhesion molecules. They are transmembrane proteins that bridge the space between adjacent epithelial cells by way of homophilic binding of their extracellular domains to other desmosomal cadherins on the adjacent cell. The desmosomal linking proteins such as desmoplakin bind to the intracellular domain of cadherins and form a connecting bridge to the cytoskeleton.

Blistering diseases

If the desmosomes connecting adjacent epithelial cells of the skin are not functioning correctly, layers of the skin can pull apart and allow abnormal movements of fluid within the skin, resulting in blisters and other tissue damage. Blistering diseases such as Pemphigus Vulgaris can be due to genetic defects in desmosomal proteins or due to an autoimmune response. These patients are often be found to have antibodies that bind to the desmosomal cadherins and disrupt the desmosomes.

Hemidesmosomes

When visualized by electron microscopy, hemidesmosomes are similar in appearance to desmosomes. Rather than linking two cells, hemidesmosomes attach one cell to the extracellular matrix. Rather than using cadherins, hemidesmosomes use integrin cell adhesion proteins.

Cytoskeleton

The cytoskeleton is a cellular "scaffolding" or "skeleton" contained within the cytoplasm. It is a dynamic structure that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (the movement of vesicles and organelles, for example) and cellular division. Eukaryotic cells contain three kinds of cytoskeletal filaments.

Actin Filaments

Actin is a globular protein that polymerize helicaly forming actin filaments (or microfilaments), which like the other two components of the cellular cytoskeleton form a three-dimensional network inside an eukariotic cell. Actin filaments provide mechanical support for the cell, determine the cell shape, enable cell movements (through pseudopods); and participate in certain cell junctions, in cytoplasmic streaming and in contraction of the cell during cytokinesis. In muscle cells they play an essential role, along with myosin, in muscle contraction. In the cytosol, actin is predominantly bound to ATP, but can also bind to ADP. An ATP-actin complex polymerizes faster and dissociates slower than an ADP-actin complex. Actin is also one of the most highly conserved proteins, differing by no more than 5% in species as diverse as algae and humans.

Microfilaments assembly

The globular Actin is known as G-actin, while the filamentous polymer composed of G-actin subunits (a microfilament), is called F-actin. The microfilaments are the thickest of the cytoskeleton, with only 7nm in diameter. Much like the microtubules, actin filaments are polar, with the plus (+) end elongating approximately 10 times faster than the minus (-) end. The process of actin polymerization, nucleation, starts with the association of three G-actin monomers into a trimer. ATP-actin then binds the plus (+) end, and the ATP is subsequently hydrolyzed, which reduces the binding strength between neighboring units and generally destabilizes the filament. ADP-actin dissociates from the minus end and the increase in ADP-actin stimulates the exchange of bound ADP for ATP, leading to more ATP-actin units. This rapid turnover is important for the cells movement.

The protein cofilin binds to ADP-actin units and promotes their dissociation from the minus end and prevents their reassembly. The protein profilin reverses this effect by stimulating the exchange of bound ADP for ATP. In addition, ATP-actin units bound to profilin will dissociate from cofilin and are then free to polymerize. Another important component in filament production is the Arp2/3 proteins, which serve as sites for nucleation, stimulating the formation of G-actin trimers. All of these three proteins are regulated by cell signaling mechanism.

Actin filaments are assembled in two general types of structures: bundles and networks. Actin-binding proteins dictate the formation of either structure since they cross-link actin filaments. Actin filaments have the appearance of a double-stranded helix.

Bundles

There are two types of actin bundles: parallel and contractile bundles. In parallel bundles, the filaments are spaced 14nm apart by the actin-bundling proteins fimbrin. Parallel bundles are responsible for the supporting a cells microvilli. In vertebrates, the actin-bundling protein villin is almost entirely found in the microvilli of intestinal cells.

Together with myosin filaments actin it forms Actomyosin, which provides the mechanism for muscle contraction. Actin uses ATP for energy. The ATP allows, through hydrolysis, the myosin head to extend up and bind with the actin filament. The myosin head then releases after moving the actin filament in a relaxing or contracting movement by usage of ADP.

In contractile bundles, the actin-bundling protein actinin separates each filament by 40nm. This increase in distance allows the motor protein myosin to interact with the filament, enabling deformation or contraction. In the first case, one end of myosin is bound to the plasma membrane while the other end walks towards the plus end of the actin filament. This pulls the membrane into a different shape relative to the cell cortex. For contraction, the myosin molecule is usually bound to two separate filaments and both ends simultaneously walk towards their filament's plus end, sliding the actin filaments over each other. This results in the shorterning, or contraction, of the actin bundle (but not the filament). This mechanism is responsible for muscle contraction and cytokinesis, the division of one cell into two.

Networks

Actin networks, along with their actin-binding protein, filamin , form the cells cortex. This underlies the plasma membrane and is responsible for the shape of the cell.

Intermediate Filaments

These 8 to 11 nanometers in diameter filaments are the more stable (strongly bound) and heterogenous constitutents of the cytoskeleton. They organize the internal tridimensional structure of the cell (they are structural components of the nuclear envelope or the sarcomeres for example). Their size is intermediate between that of microfilaments and microtubules. They are assembled from several different proteins. IFs crisscross the cytosol from the nuclear envelope to the cell membrane. They also participate in some cell-cell and cell-matrix junctions.

Different intermediate filaments are:

vimentins, being the common structural support of many cells.

keratin, found in skin cells, hair and nails.

Neurofilaments of neural cells.

Lamin, giving structural support to the nuclear envelope.

Microtubules

They are hollow cylinders of about 25 nm., formed by 13 protofilaments which, in turn, are polymers of alpha and beta tubulin (a potein). They have a very dynamic behaviour, binding GTP for polymerization, they are organized by the centrosome.

They play key roles in:

Intracellular transport (asociated with dyneins and kinesins they transport organelles like mitochondria or vesicles.)

the axoneme of cilia and flagella

the mitotic spindle

Microtubules are part of a structural network (the cytoskeleton) within the cell's cytoplasm, but in addition to structural support microtubules are used in many other processes as well. They are capable of growing and shrinking in order to generate force, and there are also motor proteins that move along the microtubule. A notable structure involving microtubules is the mitotic spindle used by eukaryotic cells to segregate their chromosomes correctly during cell division. Microtubules are also responsible for the flagella of eukaryotic cells (prokaryote flagella are entirely different).

Dynamic Instability

Tubulin binds GTP in order to assemble onto the (+) end of a microtubule. Shortly after assembly, the GTP is hydrolyzed to GDP. A GDP-bound tubulin subunit at the tip of a microtubule will fall off, though a GDP-bound tubulin in the middle of a microtubule cannot spontaneously pop out. Since tubulin adds onto the end of the microtubule only in the GTP-bound state, there is generally a cap of GTP-bound tubulin at the tip of the microtubule, protecting it from disassembly. When hydrolysis catches up to the tip of the microtubule, it begins a rapid depolymerization and shrinkage. This switch from growth to shrinking is called a catastrophe. GTP-bound tubulin can begin adding to the tip of the microtubule again, providing a new cap and protecting the microtubule from shrinking. This is referred to as rescue.

The drug taxol, used in the treatment of cancer, blocks dynamic instability by stabilizing GDP-bound tubulin in the microtubule. Thus, even when hydrolysis of GTP reaches the tip of the microtubule, there is no depolymerization and the microtubule does not shrink back. Colchicine has the opposite effect: it blocks the polymerization of tubulin into microtubules.

Motor Proteins

In addition to movement generated by the dynamic instability of the microtubule itself, the fibers are substrates along which motor proteins can move. The major microtubule motor proteins are kinesin and dynein.

Cilium

A cilium (plural cilia) is a fine projection from a cell. There are two types of cilia: (1) motile cilium, which constantly beats in one direction, and (2) non-motile cilium, which cannot beat and usually serves as a sensor.

Cilia are structurally identical to eukaryotic flagella, and the two terms are often used interchangeably. In general, though, the term cilia is used when they are numerous, short and coordinated while flagella is used when they are relatively sparse and long. The name cilium may also be used to emphasize their differences from bacterial flagella.

Motile cilia are almost never found alone, usually being present on a cell's surface in large numbers that beat coordinately in unified waves. In humans, for example, motile cilia are found in the lining of the trachea or windpipe, where they sweep mucus and dirt out of the lungs. In the oviducts, the beating of cilia moves the ovum from the ovary to the uterus.

Opposite to the motile cilia, non-motile cilium usually exists as one cilium per cell. The outer segment of the rod photoreceptor cell in the human eye is connected to its cell body with a specialized non-motile cilium. The terminal fiber of the olfactory neuron is also a non-motile cilium, where the odorant receptors locate. Almost all types of the mammalian cells have a single non-motile cilium called "Primary cilium" that has been neglected for a long time. Recent studies led scientists to re-evaluate its physiological role(s) in the cell signaling and the control of cell growth and development.

A cilium has an outer membrane that surrounds a core called an axoneme, which contains nine pairs of microtubule doublets and other associated proteins. Motile cilia have a central core with two additional microtubule singlets and dynein motor proteins which are attached to the outer microtubule doublets. Biologists refer to this organization as a cononical "9 + 2" structure. The non-motile cilia do not have the two central microtubule singlets and do not have dyneins. This configuration of axoneme is referred as a "9 + 0" type. At the base of the cilium is its microtubule organization center called a basal body. Basal body is structurally identical to and functionally interchangeable with centriole in the animal cells. The region between the basal body and axoneme is a short transition zone which is less studied.

A defect in the cilium can cause human disease. The best known cilia-related disorder is Primary Ciliary Dyskinesia (PCD). In addition, a defect of the primary cilium in the renal tube cells can lead to polycystic kidney disease (PKD). In another genetic disorder called Bardet-Biedl syndrome (BBS), the mutant gene products are the components in the basal body and cilia.

Dynein

Dynein is a class of protein and can be divided into two groups: cytoplasmic dynein and axonemal dynein. The axonemal dynein acts to activate a sliding within flagellar microtubules, whereas the cytoplasmic dynein is implicated in moving toward the negative end of a microtubule.

Kinesin

Kinesins typically consist of two large globular heads that allow attachment to microtubules, a central coiled region, and a region termed light-chain, which connects the kinesin to the intracellular component to be moved.

Kinesin and Dynein belong to Microtubule Associated Proteins (MAPs). These motor MAPs attach both to intracellular components, and to microtubles (MTs), and by moving along the MT they are able to transport the intracellular components, which could be organelles, or vesicles, to where they are required.

Cytoplasm

Cytoplasm is the colloidal, semi-fluid matter contained within the cell's plasma membrane, in which organelles are suspended. In contrast to the protoplasm, the cytoplasm does not include the cell nucleus, the interior of which is made up of nucleoplasm.

Components of the cytoplasm

The aqueous component of the cytoplasm (making up 80 percent of it) is composed of ions and soluble macromolecules like enzymes, carbohydrates, different salts and proteins, as well as a great proportion of ARN. The cytoplasm's watery component is also known as hyaloplasm .

The watery component can be more or less gel-like or liquid depending on the milieu's conditions and the activity phases of the cell. In the first case, it is named cytogel and is a viscid solid mass. In the second case, called cytosol, is a liquid in movement. In general, margin regions of the cell are gel-like and the cell's interior is liquid.

The insoluble constituents of the cytoplasm are organelles (such as the mitochondria, the lysosomes HYPERLINK "http://www.biologydaily.com/biology/Chloroplast"

, peroxysomes, ribosomes), several vacuoles, cytoskeletons as well as complex membrane structures (e.g. endoplasmic reticulums or the golgi apparatus).

Function

The cytoplasm plays a mechanical role, i.e. to maintain the shape, the consistency of the cell and to provide suspension to the organelles. It is also a storage place for chemical substances indispensable to life. Vital metabolic reactions take place here, for example anaerobic glycolysis and proteic synthesis.

Cytosol

The cytosol (as opposed to cytoplasm, which also includes the organelles) is the internal fluid of the cell, and a large part of cell metabolism occurs here. Proteins within the cytosol play an important role in signal transduction pathways, glycolysis, and they act as intracellular receptors and ribosomes. In prokaryotes, all chemical reactions take place in the cytosol. In eukaryotes, the cytosol contains the cell organelles. The cytosol is not a "soup" with free-floating particles, but is highly organized on the molecular level. The cytosol also contains the cytoskeleton. This is made of fibrous proteins (microfilaments, microtubules, and intermediate filaments) and (in many organisms) maintains the shape of the cell, anchors organelles, and controls internal movement of structures, e.g., transport vesicles.

As the concentration of soluble molecules increases within the cytosol, an osmotic gradient builds up toward the outside of the cell. Water flows into the cell, making the cell larger. To prevent the cell from bursting apart, molecular pumps in the plasma membrane, the cytoskeleton, the tonoplast or the cell wall (if present), are used to counteract the osmotic pressure. Details

The cytosol is 20% to 30% protein.

Normal human cytosolic pH is (roughly) 7.0 (i.e. neutral), whereas the pH of the extracellular fluid is 7.4.

Vesicle

A vesicle is a relatively small and enclosed compartment, separated from the cytosol by at least one lipid bilayer. Vesicles store, transport, or digest cellular products and wastes.

This biomembrane enclosing the vesicle is the same as that of the outer (cellular) membrane. Thus, because of the separation, the intravesicular environment can be made to be different from the cytosolic environment. Vesicles are a basic tool of the cell for organizing metabolism, transport, enzyme storage, as well as being chemical reaction chambers. Many vesicles are made in the Golgi apparatus, but also in the endoplasmic reticulum, or are made from parts of the plasma membrane.

Lysosomes (membrane-bound digestive vesicles) can digest macromolecules (break them down to small compounds) that were taken in from the outside of the cell by an endocytic vesicle. This is the basic way for a cell to feed (except for photosynthesis in plants, which don't have lysosomes). The membrane of the lysosome is impermeable for lysozyme, the enzyme that does the actual digestion, to protect the cell interior from being digested by its own enzyme. Lysosomes are made in the Golgi apparatus.

Neurons store neurotransmitters in synaptic vesicles located at presynaptic terminals.

Transport vesicles

Transport vesicles can move molecules between locations inside the cell, e.g., proteins from the endoplasmic reticulum to the Golgi apparatus, and from there to the outer cell membrane, where they are secreted. They do this by budding off from one compartment and joining to another. Anterograde transport vesicles : These are forward-moving vesicles.

Retrograde transport vesicles : These vesicles move from later to earlier cisterna.

Vesicles can be used as reaction chambers for chemical reactions that could damage the cell if they would occur in the cytosol. For example, peroxisomes are detoxifiers of hydrogen peroxide (H2O2), a toxic byproduct of cell metabolism. Large storage vesicles are known as vacuoles.

Mechanisms

Assembly of a protein coat drives vesicle formation and selection of cargo molecules.

Vesicle coat

The vesicle coat serves to sculpt the curvature of a donor membrane, and to select specific proteins as cargo. It selects cargo proteins by binding to sorting signals . In this way the vesicle coat clusters selected membrane cargo proteins into nascent vesicle buds.

Organelle

An organelle is one of several structures with specialized functions, suspended in the cytoplasm of a eukaryotic cell. Organelles were historically identified through the use of some form of microscopy and were also identified through the use of cell fractionation.

Organelles include:

mitochondrion

endoplasmic reticulum

golgi apparatus

lysosome

myofibril

centriole nucleus peroxisome ribosome vacuole vesicle MitochondriaA mitochondrion (from Greek mitos thread + khondrion granule) is an organelle found in most eukaryotic cells, including those of plants, animals, fungi. Usually a cell has hundreds or thousands of mitochondria. The exact number of mitochondria depends on the cell's level of metabolic activity: more activity means more mitochondria. Mitochondria can occupy up to 25% of the cell's cytosol. Mitochondria are sometimes described as "cellular power plants", because their primary function is to convert organic materials into energy in the form of ATP.

Mitochondrion structure

Cross-section of a mitochondrion, showing: (1) inner membrane, (2) outer membrane, (3) cristae, (4) matrix

Depending on the cell type, mitochondria can have very different overall structures. At one end of the spectrum, the mitochondria can resemble the standard sausage-shaped organelle pictured to the right, ranging from 1 to 4 m in length. At the other end of the spectrum, mitochondria can appear as a highly branched, interconnected tubular network. Observations of fluorescently labelled mitochondria in living cells have shown them to be dynamic organelles capable of dramatic changes in shape. Finally, mitochondria can fuse with one another, or split in two.

The outer boundary of a mitochondrion contains two functionally distinct membranes: the outer mitochondrial membrane and the inner mitochondrial membrane. The outer mitochondrial membrane completely encloses the organelle, serving as its outer boundary. The inner mitochondrial membrane is thrown into folds, or cristae, that project inward. The cristae surface houses the machinery needed for aerobic respiration and ATP formation, and their folded form increases that capacity by increasing the surface area of the inner mitochondrial membrane.

The membranes of the mitochondrion divide the organelle into two distinct compartments: one within the interior of the mitochondrion, called the matrix, and a second between the inner and outer membranes, called the intermembrane space.

The mitochondrial membranes

The outer and inner membranes are composed of phospholipid bilayers studded with proteins, much like a typical cell membrane. The two membranes, however, have very different properties. The outer mitochondrial membrane, which encloses the entire organelle, is composed of about 50% phospholipids by weight and contains a variety of enzymes involved in such diverse activities such as the oxidation of epinephrine (adrenaline), the degradation of tryptophan, and the elongation of fatty acids.

The inner mitochondrial membrane, in contrast, contains more than 100 different polypeptides, and has a very high protein to phospholipid ratio (more than 3:1 by weight, which is about 1 protein for 15 phospholipids). Additionally, the inner membrane is rich in a an unusual phospholipid, cardiolipin , which is usually characteristic of bacterial plasma membranes.

The outer mitochondrial membrane contains numerous integral proteins called porins, which contain a relatively large internal channel (about 2-3 nm) and allow ions and small molecules to move in and out of the mitochondrion. Large molecules, however, cannot traverse the outer membrane. The inner membrane does not contain porins, however, and is highly impermeable; almost all ions and molecules require special membrane transporters to enter or exit the matrix.

The mitochondrial matrix

In addition to various enzymes, the mitochondrial matrix also contains ribosomes and several molecules of DNA. Thus, mitochondria possess their own genetic material, and the machinery to manufacture their own RNAs and proteins. (See: protein synthesis). This nonchromosomal DNA encodes a small number of mitochondrial peptides (13 in humans) that are integrated into the inner mitochondrial membrane, along with polypeptides encoded by genes that reside in the host cell's nucleus.

Mitochondrial functions

Although the primary function of mitochondria is to convert organic materials into cellular energy in the form of ATP, mitochondria play an important role in many important metabolic tasks, such as: Apoptosis

Glutamate-mediated excitotoxic neuronal injury

Cellular proliferation

Regulation of the cellular redox state

Heme synthesis

Steroid synthesis

Heat production (enabling the organism to stay warm)

Some mitochondrial functions are performed only in specific types of cells. For example, mitochondria in liver cells contain enzymes that allow them to detoxify ammonia, a waste product of protein metabolism. A mutation in the genes regulating any of these functions can result in a variety of mitochondrial diseases.

Energy conversion

As stated above, the primary function of the mitochondria is the production of ATP. This is done by metabolizing the major products of glycolysis, pyruvate and NADH (glycolysis is performed outside the mitochondria, in the host cell's cytosol). This metabolism can be performed in two very different ways, depending on the type of cell and the presence or absence of oxygen.

Adenosine triphosphate (ATP) is the nucleotide known in biochemistry as the "molecular currency" of intracellular energy transfer; that is, ATP is able to store and transport chemical energy within cells. ATP also plays an important role in the synthesis of nucleic acids. ATP molecules are also used to store the energy plants make in cellular respiration.

Chemical properties Chemically, ATP consists of adenosine and three phosphate groups. It has the empirical formula C10H16N5O13P3, and the chemical formula C10H8N4O2NH2(OH)2(PO3H)3H, with a molecular mass of 507.184 u. The phosphoryl groups starting with that on AMP are referred to as the alpha, beta, and gamma phosphates. The biochemical name for ATP is 9--D-ribofuranosyladenine-5'-triphosphate.

Synthesis ATP can be produced by various cellular processes, most typically in mitochondria by oxidative phosphorylation under the catalytic influence of ATP synthase. The main fuels for ATP synthesis are glucose and fatty acids. Initially glucose is broken down into pyruvate in the cytosol. Two molecules of ATP are generated for each molecule of glucose. The terminal stages of ATP synthesis are carried out in the mitochondrion and can generate up to 36 ATP.

ATP in the human body The total quantity of ATP in the human body is about 0.1 mole. The energy used by human cells requires the hydrolysis of 200 to 300 moles of ATP daily. This means that each ATP molecule is recycled 2000 to 3000 times during a single day. ATP cannot be stored, hence its synthesis must closely follow its consumption.

Other triphosphates Living cells also have other "high-energy" nucleoside triphosphates, such as guanosine triphosphate. Between them and ATP, energy can be easily transferred with reactions such as those catalyzed by nucleoside diphosphokinase : Energy is released when hydrolysis of the phosphate-phosphate bonds is carried out. This energy can be used by a variety of enzymes, motor proteins , and transport proteins to carry out the work of the cell. Also, the hydrolysis yields free inorganic phosphate and adenosine diphosphate, which can be broken down further to another phosphate ion and adenosine monophosphate. ATP can also be broken down to adenosine monophosphate directly, with the formation of pyrophosphate. This last reaction has the advantage of being an effectively irreversible process in aqueous solution.

Reaction of ADP with GTP

ADP + GTP ATP + GDP

There is talk of using ATP as a power source for nanotechnology and implants. Artificial pacemakers could become independent of batteries.

Pyruvate: the Krebs cycle

Each pyruvate molecule produced by glycolysis is actively transported across the inner mitochondrial membrane, and into the matrix where it is combined coenzyme A to form acetyl CoA. Once formed, acetyl CoA is fed into the Krebs cycle, also known as the tricarboxylic acid (TCA) cycle or citric acid cycle. This process creates 3 molecules of NADH and 1 molecule of FADH2, which go on to participate in the electron transport chain. With the exception of succinate dehydrogenase, which is bound to the inner mitochondrial membrane, all of the enzymes of the Krebs cycle are dissolved in the mitochondrial matrix.

NADH and FADH2: the electron transport chain

This energy from NADH and FADH2 is transferred to oxygen (O2) in several steps involving the electron transfer chain. The protein complexes in the inner membrane (NADH dehydrogenase, cytochrome c reductase, cytochrome c oxidase) that perform the transfer use the released energy to pump protons (H+) against a gradient (the concentration of protons in the intermembrane space is higher than that in the matrix). An active transport system (energy requiring) pumps the protons against their physical tendency (in the "wrong" direction) from the matrix into the intermembrane space.

As the proton concentration increases in the intermembrane space, a strong diffusion gradient is built up. The only exit for these protons is through the ATP synthase complex. By transporting protons from the intermembrane space back into the matrix, the ATP synthase complex can make ATP from ADP and inorganic phosphate (Pi). This process is called chemiosmosis and is an example of facilitated diffusion. Peter Mitchell was awarded the 1978 Nobel Prize in Chemistry for his work on chemiosmosis. Later, part of the 1997 Nobel Prize in Chemistry was awarded to Paul D. Boyer and John E. Walker for their clarification of the working mechanism of ATP synthase.

Use in population genetic studies

Because eggs (ovum) destroy the mitochondria of the sperm that fertilize them, the mitochondrial DNA of an individual derives exclusively from the mother. Individuals inherit the other kinds of genes and DNA from both parents jointly. Because of the unique matrilineal transmission of mitochondrial DNA, scientists in population genetics and evolutionary biology often use data from mitochondrial DNA sequences to draw conclusions about genealogy and evolution.

The endosymbiotic theory

Mitochondria are unusual among organelles in that they contain ribosomes and their own genetic material. Mitochondrial DNA is circular and employs characteristic variants of the standard eukaryotic genetic code.

These and similar pieces of evidence motivate the endosymbiotic theory that mitochondria originated as prokaryotic endosymbionts. Essentially this widely accepted hypothesis postulates that the ancestors of modern mitochondria were independent bacteria that colonized the interior of the ancient precursor of all eukaryotic life.

Ribosome

Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). Side and front view. (1) Head. (2) Platform. (3) Base. (4) Ridge. (5) Central protuberance. (6) Back. (7) Stalk. (8) Front.

A ribosome is an organelle composed of rRNA (synthesized in the nucleolus) and ribosomal proteins. It translates mRNA into a polypeptide chain (e.g., a protein). It can be thought of as a factory that builds a protein from a set of genetic instructions. Ribosomes can float freely in the cytoplasm (the internal fluid of the cell) or bind to another organelle called the endoplasmic reticulum. Since ribosomes are ribozymes, it is thought that they might be remnants of the RNA world.

Ribosomes consist of two subunits (Figure 1) that fit together (Figure 2) and work as one to translate the mRNA into a polypeptide chain during protein synthesis (Figure 3). Each subunit consists of one or two very large RNA molecules (known as ribosomal RNA or rRNA) and multiple smaller protein molecules. Experiments have shown that the rRNA are the crucial components in protein synthesis, and that one aspect of the process, peptide transfer, can occur in the presence of rRNA alone, albeit at a slower rate. This suggests that the protein components of ribosomes act as a scaffold that may enhance the ability of rRNA to synthesise protein.

The structure and function of ribosomes, and their attendant molecules, known as the translational apparatus, has been of ongoing research interest since the mid 20th century on through the early 21st century. A triennial conference is held to discuss the ribosome. In 1999, the conference was held in Elsinore, Denmark. The 2002 conference was held in Queenstown, New Zealand [1].

Figure 2: Large (1) and small (2) subunit fit together

Free ribosomes

Free ribosomes occur in all cells, and also in mitochondria and chloroplasts in eukaryotic cells. Several free ribosomes can associate on a single mRNA molecule to form a polyribosome or polysome. Free ribosomes usually produce proteins that are used in the cytosol or in the organelle they occur in.

Membrane bound ribosomes

When certain proteins are synthesized by a ribosome, it can become "membrane-bound", associated with the membrane of the nucleus and the rough endoplasmic reticulum (in eukaryotes only) for the time of synthesis. They insert the freshly produced polypeptide chains directly into the ER, from where they are transported to their destinations. Bound ribosomes usually produce proteins that are used within the cell membrane or are expelled from the cell via exocytosis.

The ribosomal subunits of prokaryotes and eukaryotes are quite similar. However, prokaryotes use 70S ribosomes, each consisting of a (small) 30S and a (large) 50S subunit, whereas eukaryotes use 80S ribosomes, each consisting of a (small) 40S and a bound (large) 60S subunit.[The unit S means Svedberg units, a measure of the rate of sedimentation of a particle in a centrifuge, where the sedimentation rate is associated with the size of the particle. Svedberg units are not additive - two subunits together can have Svedberg values that do not add up to that of the entire ribosome.]

Figure 3: Translation (1) of mRNA by a ribosome (2) into a polypeptide chain (3). The mRNA begins with a start codon (AUG) and ends with a stop codon (UAG).

In Figure 3, both ribosomal subunits (small and large) assemble at the start codon (the 5' end of the mRNA). The ribosome uses tRNA (transfer RNAs which are RNA molecules that carry an amino acid and present the matching anti-codon, according to the genetic code, to the ribosome) which matches the current codon (triplet) on the mRNA to append an amino acid to the polypeptide chain. This is done for each triplet on the mRNA, while the ribosome moves towards the 3' end of the mRNA. Usually, several ribosomes are working parallel on a single mRNA.

Endoplasmic reticulum

The endoplasmic reticulum or ER (endoplasmic means "within the cytoplasm", reticulum means "little net") modifies proteins, makes macromolecules, and transfers substances throughout the cell. Prokaryotic organisms do not have organelles and thus do not have an ER. ER's base structure and composition is similar to the plasma membrane, though it is an extension of the nuclear membrane. The ER is the site of the translation and folding of and transport of proteins that are to become part of the cell membrane (e.g., transmembrane receptors and other integral membrane proteins) as well as proteins that are to be secreted or "exocytosed" from the cell (e.g., digestive enzymes).

Structure

Figure 1: Image of nucleus, endoplasmic reticulum and Golgi apparatus.(1) Nucleus. (2) Nuclear pore. (3) Rough endoplasmic reticulum (RER). (4) Smooth endoplasmic reticulum (SER). (5) Ribosome on the rough ER. (6) Proteins that are transported. (7) Transport vesicle. (8) Golgi apparatus. (9) Cis face of the Golgi apparatus. (10) Trans face of the Golgi apparatus. (11) Cisternae of the Golgi apparatus.

The ER consists of an extensive membrane network of tubes and cisternae (sac-like structures). The membrane encloses a space, the cisternal space (or internal lumen) from the cytosol. This space is acting as a gateway. Parts of the ER membrane are continuous with the outer membrane of the nuclear envelope, and the cisternal space of the ER is continuous with the space in between the two layers of the nuclear envelope.

Parts of the ER are covered with ribosomes (which assemble amino acids into proteins based on instructions from the nucleus). Their rough appearance under electron microscopy led to their being called rough ER (RER), other parts are free of ribosomes and are called smooth ER (SER). The ribosomes on the surface of the rough ER insert the freshly produced proteins directly into the ER, which processes them and then passes them on to the Golgi apparatus (Fig. 1). Rough and smooth ER differ not only in appearance, but also in function.

Rough ERThe coarse ER manufactures and transports proteins destined for membranes and secretion. It synthesizes membrane, organellar, and excreted proteins. Minutes after proteins are synthesized most of them leave to the Golgi apparatus within vesicles. The rough ER also modifies, folds, and controls the quality of proteins.

Smooth ERThe smooth ER has functions in several metabolic processes. It takes part in the synthesis of various lipids (e.g., for building membranes such as phospholipids), fatty acids and steroids (e.g., hormones), and also plays an important role in carbohydrate metabolism, detoxification of the cell (enzymes in the smooth ER detoxify chemicals), and calcium storage. It also is a large transporter of nutrient found in each cell.

FunctionsThe endoplasmic reticulum serves many general functions, including the facilitation of protein folding, and the transport of proteins. Correct folding of newly made proteins is made possible by several ER proteins including: PDI, Hsc70 family , calnexin , calreticulin, and the peptidylpropyl isomerase family . Only properly folded proteins are transported from the RER to the Golgi complex.

Transport of proteinsSecretory proteins are moved across the ER membrane. Proteins that are transported by the ER and from there throughout the cell are marked with an address tag that are called a signal sequence. Gnter Blobel was awarded the 1999 Nobel Prize in Physiology or Medicine for his discovery of these signal sequences in 1975. The N-terminus (one end) of a polypeptide chain (e.g., a protein) contains a few amino acids that work as an address tag, which are removed when the polypeptide reaches its destination. Proteins that are destined for places outside the ER are packed into transport vesicles and moved along the cytoskeleton towards their destination. The ER is also part of a protein sorting pathway.

Other functions Insertion of proteins into the ER membrane. Integral proteins need to be inserted into the ER membrane after they are synthesized. Insertion into the ER membrane requires the correct topogenic sequences.

Glycosylation. Glycosylation involves the attachment of oligosaccharides.

Disulfide bond formation and rearrangement. Disulfide bonds stabilize the tertiary and quaternary structure of many proteins.

Sarcoplasmic reticulum. The endoplasmic reticulum found in muscle fibers is called sarcoplasmic reticulum.

Categories: OrganellesGolgi apparatus

The Golgi apparatus (Golgi body, Golgi complex, or dictyosome) is an organelle found in most eukaryotic cells, including those of plants and animals (but not most fungi). The name comes from Italian anatomist Camillo Golgi, who identified it in 1898. Its primary function is to process proteins targeted to the plasma membrane, lysosomes or endosomes and those that will be secreted from the cell, and sort them within vesicles. Thus, it functions as a central delivery system for the cell.

Most of the transport vesicles that leave the endoplasmic reticulum (ER), specifically rough ER, are transported to the Golgi apparatus, where they are modified, sorted and shipped towards their final destination. The Golgi apparatus is present in most eukaryotic cells, but tends to be more prominent where there are a lot of substances, such as enzymes, being secreted.

Structure

Figure 1: Image of nucleus, endoplasmic reticulum and Golgi apparatus: (1) Nucleus, (2) Nuclear pore, (3) Rough endoplasmic reticulum (RER), (4) Smooth endoplasmic reticulum (SER), (5) Ribosome on the rough ER, (6) Proteins that are transported, (7) Transport vesicle, (8) Golgi apparatus, (9) Cis face of the Golgi apparatus, (10) Trans face of the Golgi apparatus, (11) Cisternae of the Golgi apparatus, (12) Secretory vesicle, (13) Plasma membrane, (14) Exocytosis, (15) Cytoplasm, (16) Extracellular space.

The structure and internal function of the Golgi apparatus is quite complex and is the subject of scientific dispute. The Golgi apparatus consists, like the ER, of membranous structures. It is made up of a stack of flattened cisternae and similar vesicles. The cis face is the side facing the ER, the medial region is in the middle while the trans face is directed towards the plasma membrane (Fig. 1). The cis and trans faces have different membranous compositions.

FunctionThe transport vesicles from the ER fuse with the cis face of the Golgi apparatus (to the cisternae) and empty their protein content into the Golgi lumen. The proteins are then transported through the medial region towards the trans face and are modified on their way.

The transport mechanism itself is not yet clear; it could happen by cisternae progression (the movement of the apparatus itself, building new cisternae at the cis face and destroying them at the trans face) or by vesicular transport (small vesicles transport the proteins from one cisterna to the next, while the cisternae remain unchanged). Lately, it is also proposed that the cisternae are interconnected and the transport of cargo molecules within the Golgi is due to diffusion, while the localisation of Golgi resident proteins is achieved by an unknown mechansim.

Once the proteins reach the trans face, they are embedded into coated transport vesicles and brought to their final destinations. An example is the modification of glycoproteins (used in cell membranes). Vesicles from the ER contain simplified glycosylated proteins. In the Golgi Apparatus, carbohydrates are attached and removed from these glycoproteins, creating a diversity of carbohydrate structures on the proteins. After they have been secreted in to the cell the vesicles fuse to the cell membrane and release their contents.

As well as protein modification, Golgi apparatus is involved in the transport of lipids around the cell as well creating lysosomes -- organelles involved in digestion.

Categories: Organelles | Eponymous anatomical structuresLysosome

Lysosomes are organelles that contain digestive enzymes to digest macromolecules. They are built in the Golgi apparatus. At pH 4.8, the interior of the lysosomes is more acidic than the cytosol (pH 7). The lysosome single membrane stabilizes the low pH by pumping in protons (H+) from the cytosol, and also protects the cytosol, and therefore the rest of the cell, from the degradative enzymes within the lysosome. The digestive enzymes need the acidic environment of the lysosome to function correctly. All these enzymes are produced in the endoplasmic reticulum, and transported and processed through the Golgi apparatus. The Golgi apparatus produces lysosomes by budding.

The most important enzymes in lysosomes are:

Lipase, which digests lipids,

Carbohydrases , which digest carbohydrates (e.g., sugars),

Proteases, which digest proteins,

Nucleases, which digest nucleic acids.

The lysosomes are used for the digestion of macromolecules from phagocytosis (ingestion of cells), from the cell's own recycling process (where old components such as worn out mitochondria are continuously destroyed and replaced by new ones, and receptor proteins are recycled), and for autophagic cell death, a form of programmed self-destruction of the cell, which means that the cell is digesting itself. Other functions include digesting foreign bacteria that invade a cell and helping repair damage to the plasma membrane by serving as a membrane patch, sealing the wound.

There are a number of illnesses that are caused by the malfunction of the lysosomes or one of their digestive proteins, e.g., Tay-Sachs disease, or Pompe's disease. These are caused by a defective or missing digestive protein, which leads to the accumulation of substrates within the cell, resulting in impaired cell metabolism. Broadly, these can be classified as mucopolysaccharidoses, GM2 gangliosid