LEVELS OF ORGANIZATION OF LIVING SUBSTANCE. OPTICAL SYSTEMS IN BIOLOGICAL RESEARCHES. MORPHOLOGY OF THE CELL. VIRUS BIOLOGY. STRUCTURE OF HUMAN IMMUNODEFICIENCY VIRUS. CELL MEMBRANES. TRANSPORT OF SUBSTANCES THROUGH PLASMALEMA.

 

1.     Levels of organization of living substance. Optical systems in biological researches.

1.     General Biology as a science: definition, subject, tasks, importance to medicine.

2.     Medical Biology as science: definition, subject, tasks, importance to medicine.

3.     Fundanental characteristics of living things: self-renewal; self-reproduction; self-regulation.

4.     Levels of biological organization: molecular, subcellalar, cellular, tissular, organismic, level of population and species, biocenotical, biospheric. Importance of levels of biological organization for medicine.

5.     The methods of biological investigation: comparative, descriptive, experimental and historical.

6.     Light microscope structure: mechanical, optical, illuminative parts.

7.     The main principles of working with light microscope.

8.     Principles of provisional specimen preparation.

 General Biology is the synthetic science of life. A subject of biology is a life in different ways of manifestation and living things coexistence in different levels of the living organization. The main task of biology as a science is the learning of life processes conformities and as a result – to control these processes. Modern Biology is a complex of sciences about living nature (zoology, histology, botany etc.).

 

Levels of organization. Optical systems in biological objects.

All organisms are composed of cells. Some are composed of a single cell (Figure 1), and some, like us, are composed of many cells. The gossamer wing of a butterfly is a thin sheet of cells, and so is the glistening layer covering your eyes. The hamburger you eat is composed of cells, and its contents soon become part of your cells. Your eyelashes and fingernails, orange juice, the wood in your pencil – all were produced by cells. Cells are so much a part of life as we know it that we cannot imagine an organism that is not cellular iature. In the following chapters we will focus on cells in action, on how they communicate with their environment, grow, and reproduce.

Levels of Organization

Biosphere: The sum of all living things taken in conjunction with their environment. In essence, where life occurs, from the upper reaches of the atmosphere to the top few meters of soil, to the bottoms of the oceans. We divide the earth into atmosphere (air), lithosphere (earth), hydrosphere (water), and biosphere (life).

 Ecosystem: The relationships of smaller groups of organisms with each other and their environment. Scientists often speak of the interrelatedness of living things. Since, according to Darwin’s theory, organisms adapt to their environment, they must also adapt to other organisms in that environment. We can discuss the flow of energy through an ecosystem from photosynthetic autotrophs to herbivores to carnivores.

Community: The relationships between groups of different species. For example, the desert communities consist of rabbits, coyotes, snakes, birds, mice and such plants as sahuaro cactus (Carnegia gigantea), Ocotillo, creosote bush, etc. Community structure can be disturbed by such things as fire, human activity, and over-population.

 Species: Groups of similar individuals who tend to mate and produce viable, fertile offspring. We often find species described not by their reproduction (a biological species) but rather by their form (anatomical or form species).

 Populations: Groups of similar individuals who tend to mate with each other in a limited geographic area. This can be as simple as a field of flowers, which is separated from another field by a hill or other area where none of these flowers occur.

 Individuals: One or more cells characterized by a unique arrangement of DNA “information”. These can be unicellular or multicellular. The multicellular individual exhibits specialization of cell types and division of labor into tissues, organs, and organ systems.

 Organ System: (in multicellular organisms). A group of cells, tissues, and organs that perform a specific major function. For example: the cardiovascular system functions in circulation of blood.

 Organ: (in multicellular organisms). A group of cells or tissues performing an overall function. For example: the heart is an organ that pumps blood within the cardiovascular system.

 Tissue: (in multicellular organisms). A group of cells performing a specific function. For example heart muscle tissue is found in the heart and its unique contraction properties aid the heart’s functioning as a pump.

 Cell: The fundamental unit of living things. Each cell has some sort of hereditary material (either DNA or more rarely RNA), energy acquiring chemicals, structures, etc. Living things, by definition, must have the metabolic chemicals plus a nucleic acid hereditary information molecule.

 

Organelle: A subunit of a cell, an organelle is involved in a specific subcellular function, for example the ribosome (the site of protein synthesis) or mitochondrion (the site of ATP generation in eukaryotes).

Molecules, atoms, and subatomic particles: The fundamental functional levels of biochemistry.

It is thus possible to study biology at many levels, from collections of organisms (communities), to the inner workings of a cell (organelle).

 

GENERAL CHARACTERISTICS OF CELLS

 Before launching into a detailed examination of cell structure, it is useful first to gain an overview of what we would expect to find on the inside of a typical cell. What is a cell like? A bacterial cell, with its prokaryotic organization, is like a blimp, an outer framework supporting an inner membrane bag with a uniform interior. A eukaryotic cell is more like a submarine. A submarine has an outer hull open to the sea, and a watertight inner pressure hull; some eukaryotic cells also have a porous outer wall, covering a membrane that regulates the passage of water and dissolved substances. Within the submarine is a central control room; the control room of a eukaryotic cell is a central compartment called the nucleus. The power to drive a submarine comes from the engine room; similarly, a eukaryotic cell’s power comes from internal bacteria-like inclusions called mitochondria. The rooms of a submarine are divided by watertight compartments; a eukaryotic cell is also divided into separate rooms by a membrane system called the endoplasmic reticulum. A spinning propeller drives the submarine through the water; motile cells are driven by flagella, whip-like structures that undulate rapidly, driving the cell through the medium in which it is swimming.

 

Characteristics of living things

 Living things have a variety of common characteristics.

 Organization. Living things exhibit a high level of organization, with multicellular organisms being subdivided into cells, and cells into organelles, and organelles into molecules, etc.

 Homeostasis. Homeostasis is the maintenance of a constant (yet also dynamic) internal environment in terms of temperature, pH, water concentrations, etc. Much of our own metabolic energy goes toward keeping within our own homeostatic limits. If you run a high fever for long enough, the increased temperature will damage certain organs and impair your proper functioning. Swallowing of common household chemicals, many of which are outside the pH (acid/base) levels we can tolerate, will likewise negatively impact the human body’s homeostatic regime. Muscular activity generates heat as a waste product. This heat is removed from our bodies by sweating. Some of this heat is used by warm-blooded animals, mammals and birds, to maintain their internal temperatures.

 Adaptation. Living things are suited to their mode of existence. Charles Darwin began the recognition of the marvelous adaptations all life has that allow those organisms to exist in their environment.

 Reproduction and heredity. Since all cells come from existing cells, they must have some way of reproducing, whether that involves asexual (no recombination of genetic material) or sexual (recombination of genetic material). Most living things use the chemical DNA (deoxyribonucleic acid) as the physical carrier of inheritance and the genetic information. Some organisms, such as retroviruses (of which HIV is a member), use RNA (ribonucleic acid) as the carrier. The variation that Darwin and Wallace recognized as the wellspring of evolution and adaptation, is greatly increased by sexual reproduction.

 Growth and development. Even single-celled organisms grow. When first formed by cell division, they are small, and must grow and develop into mature cells. Multicellular organisms pass through a more complicated process of differentiation and organogenesis (because they have so many more cells to develop).

 Energy acquisition and release. One view of life is that it is a struggle to acquire energy (from sunlight, inorganic chemicals, or another organism), and release it in the process of forming ATP (adenosine triphosphate).

 Detection and response to stimuli (both internal and external).

 Interactions. Living things interact with their environment as well as each other. Organisms obtain raw materials and energy from the environment or another organism. The various types of symbioses (organismal interactions with each other) are examples of this.

The main methods of biological research are:

– the method of supervisioning;

– the method of biological experiment;

– historical method;

– describing mehod;

– microscopic method;

– the method of multigraded centrifusion;

– electronic microscopy;

– scanning electronic microscopy;

– electronic microscopic histochemistry;

– statistic method.

 

A MICROSCOPY OF OBJECTS 

Cells are so small that you cannot see them with the naked eye. Most eukaryotic cells are between 10 and 30 micrometers in diameter. Why can’t we see such small objects? Because when two objects are closer together than about 100 micrometers, the two light beams fill on the same “detector” cell at the rear of the eye. Only when two dots are farther apart than 100 micrometers will the beams fall on different cells, and only then can your eye resolve them – tell that they are two objects and not one.

Resolution is defined as the minimum distance that two points can be separated and still be distinguished as two separate points. One way to increase resolution is to increase magnification – to make small objects seem larger. Robert Hooke and Antonie van Leeuwenhoek were able to see very small cells by magnifying their size, so that the cells appeared larger than the 100 micrometer limit imposed by the structure of the human eye. Hooke and Leeuwenhoek accomplished this with simple microscopes, which magnified images of cells by bending light through a glass lens. To understand how such a single-lens microscope is able to magnify an image, examine Figure 2. The size of the image that falls on the picture screen of detector cells lining the back of your eye depends on how close the object is to your eye – the closer the object, the bigger the picture. Your eye, however, is not able to focus comfortably on an object closer than about 25 centimeters, because it is limited by the size and thickness of its lens. What Hooke and Leeuwenhoek did was assist the eye by interposing a glass lens between object and eye. The glass lens added additional focusing power, producing an image of the close-up object on the back of the eye. Because the object is closer, however, the image on the back of the eye is bigger than it would have been, had the object been 25 centimeters away from the eye – as big as a much larger object 25 centimeters away would have produced without the lens. You perceive the object as magnified, bigger.

The microscope consists of a plate with a single lens, a mounting pin that holds the specimen to be observed, a focusing screw that moves the specimeearer to or farther from the eye, and a specimen-centering screw.

Leeuwenhoek’s microscope, although simple in construction, is very powerful. One of Leeuwenhoek’s original specimens, a thin slice of cork, was recently discovered among his papers. The magnification of his microscope is 266 times, as good as many modern microscopes. The finest structures visible are less than 1 micrometer (1000 nanometers) in thickness. Modern microscopes use two magnifying lenses (and a variety of correcting lenses) that act like back-to-back eyes, the first lens focusing the image of the object on the second lens; the image is then magnified again by the second lens, which focuses it on the back of the eye. Microscopes that magnify in stages by using several lenses are called compound microscopes. The finest structures visible with modern compound microscopes are about 200 nanometers in thickness.

Compound light microscopes are not powerful enough to resolve many structures within cells. A membrane, for example, is only 5 nanometers thick. Why not just add another magnifying stage to the microscope, and so increase the resolving power? This approach doesn’t work, because when two objects are closer than a few hundred nanometers the light-beams of the two images start to overlap. A light beam vibrates like a vibrating string, and the only way two beams can get closer together and still be resolved is if the “wavelength” is shorter.

One way to do this is by using a beam of electrons rather than a light beam. Electrons have a much shorter wavelength, and a microscope employing electron beams has 400 times the resolving power of a light microscope. Transmission electron microscopes today are capable of resolving objects only 0.2 nanometer apart – just five times the diameter of a hydrogen atom! The specimen is prepared as a very thin section, and those areas that transmit more electrons (are less dense) show up as bright areas in the micrographs.

Transmission electron micrographs are so-called because the electrons used to visualize the specimens are transmitted by the material. A second kind of electron microscope, the scanning electron microscope, beams the electrons onto the surface of the specimen in the form of a fine probe, which passes back and forth rapidly. In images made with a scanning electron microscope, depressed areas and cracks in the specimen appear dark, whereas elevated areas such as ridges appear light. The electrons that are reflected back from the surface of the specimen, together with other electrons that the specimen itself emits as a result of the bombardment, are amplified and transmitted to a television screen, where the image can be viewed and photographed. Scanning electron microscopy yields striking three-dimensional images and has proved to be very useful in understanding many biological and physical phenomena.

So, we can say that we have many cells rather than a few large ones because small cells can be commanded more efficiently and, because of their greater relative surface area, have a greater opportunity to communicate with their environment.

There are three main levels of living organization: Microsystem, Mesosystem and Macrosystem. Each of them has its subordinate organization levels. Microsystem has molecular, subcellalar, cellular levels; Mesosystem has tissular, organellic, organismic levels; Macrosystem has level of population and species, biocenotical, biospheric levels.

The life of each level is determined by the structure of level situated below. A great likeness of discrete units is observed on the low levels, but with every other level the difference between discrete units increases.

Uniformity of discrete units is typical for molecular level; though nucleic acids, proteins differ greatly in different organisms. Fats and carbohydrates have similar composition. DNA (deoxyribonucleic acid) contains hereditary information. Reproduction of DNA molecules takes place at the molecular level and secures transferring of hereditary information from generation to generation, individual and specific features of organism structure and vital activity.

Constructions typical for all organisms are observed at the cellular level. Cell is an independent functional elementary unit of living thing. On the second level metabolism and energy metabolism as well as realization of hereditary information takes place.

Tissular and organellic levels occurred due to appearance of multicellular animals. They were formed at early stages of ontogenesis. There is no great variety of discrete units, i.e. tissues on this level. Plants have six main types of tissues and animals have five main types of them.

Organism is an elementary unit of life. On the organismic level different stages of ontogenesis are formed, hereditary information realizes as phenotypic signs, that are material for natural selection.

Population is a group of the same species, it is an elementary unit of evolution. On the population-species level changes that occurred at the previous levels lead to real evolutionary transformations or microevolutions.

On the level of biogeocenosis life is presented with complicated complexes of different organisms. Interactions between them are on the stage of mobile equilibrium with respect to one another and to abiotic factors of surrounding. On this level rotation of substances takes place. Biogeocenosis is an elementary unit of energy stream and rotation of substances.

Totality of biogeocenosis forms biosphere. All material and energetic rotations of biogeocenosis form a large biospherical rotation (cycle).

Thus, each level of organization has its specific ways of interaction between units specific for each level. Mechanisms of interaction, typical for the lower level remain though new types of interaction become leading. Physicians should know levels of living world organization. It allows to examine a human being organism as an integrated unity and consider it to be an elementary unit of human beings populations, realize place of human in biogeocenosis and biosphere in general.

 Microscoping — the basic method of study of preparation—utilized in biology already has been more than 300 years. There are two main kinds of modern microscopes: 1) light microscope and 2) electron microscope. In the light microscope light rays passing through a specimen are brought to focus by a set of glass lenses, and the resulting image is then viewed by the human eye. In the transmission electron microscope, electrons passing through a specimen are brought to a focus by a set of magnetic lenses, and the resulting image is projected onto a flujrescent screen or photographic film.

The structure of light microscope

1 – base plate; 2 – stand; 3 – tube object, 4 – microscope (object) stage; 5 – opening of object stage; 6 – screws of object stage; 7 – ocular (eyepiece); 8 – turret (revolting nosepiece); 9 – objectives; 10 – macrometer screw; 11 – micrometer screw; 12 – condenser; 13 – condenser screw; 14 – diaphragm; 15 – refractor (mirror).

  

Morphology of the cell. Structural components of nucleus and cytoplasm.

1.     The Cell Theory in its modern form. Importance for medicine.

2.     Cellular level of life organization: prokaryotic and eukaryotic cells.

3.     The common functions and structures of cells: cytoplasm, nucleus and cell membrane.

4.     Structural compounds of cytoplasm: cytosceleton, organelles and inclusions.

5.     Nucleus: nuclear envelope, nucleoplasm, nucleolus and chromatin.

6.     Organelles for general and for special prescription, their structure and functions.

7.     Inclusions: trophic, secretary and special.  

 Cell theory, in its modern form, includes the following principles:

1.   Cell is elementary structural and functional unit of living things, within which the life processes of metabolism and heredity occur.

2.   Cell is the unit of development of all organisms.

3.   Cells are similar in all organisms.

4.   Cell can be formed only by division of previously existing cell.

5.   Multicellular organism is composed of many cells, which form tissues, tissues form organs, organs form systems of organs, which neuroendocrine system regulates.

 

THE STRUCTURE OF SIMPLE CELLS: BACTERIA

 Bacteria are the simplest cellular organisms. Over 2500 species that have been giveames are considered to be distinct, but doubtless many times that number actually exist and have not yet been described properly. Although these species are diverse in form (Figure 3), their organization is fundamentally similar: small cells about 1 to 10 micrometers thick, enclosed within a membrane and encased within a rigid cell wall, with no distinct interior compartments. Sometimes the cells of bacteria adhere in chains or masses, but fundamentally the individual cells are separate from one another.

Our conclusion is: compared with the other kinds of cells that have evolved from them, bacteria are smaller and lack interior organization.

A typical cell, then, is composed of the following three elements:

1. A membrane surrounds the cell, isolating it from the outside world. Later we will describe the many passageways and communications channels that span these membranes. They provide the only connection between the cell and the outside world.

2. The nuclear region directs the activities of the cell. In bacteria, the genetic material is mostly included in a single, closed, circular molecule of DNA, which resides in a central portion of the cell, unbounded by membranes. In eukaryotes, by contrast, a double membrane – the nuclear membrane, surrounds the nucleus.

3. A semifluid matrix called the cytoplasm occupies the volume between the nuclear region and the cell membrane. In bacteria, the cytoplasm contains the chemical wealth of the cell, the sugars, amino acids, and proteins that the cell uses to carry out its everyday activities of growth and reproduction. In addition to these elements, the cytoplasm of a eukaryotic cell contains numerous organized structures, called organelles. Many of these organelles are created by the membranes of the endoplasmic reticulum, which close off compartments within which different activities take place. The cytoplasm of eukaryotic cells also contains bacteria-like organelles, called mitochondria that provide power for the cell.

All cells share this architecture. In different broad classes of cells, however, the general plan is modified in various ways. For example, the cells of most kinds of organisms – plants, bacteria, fungi, some protists – possess an outer cell wall that provides structural strength, whereas animal cells do not. The cells of plants frequently contain large membrane-bound sacs called central vacuoles, which are used for storage of proteins and waste chemicals; vacuoles in animal cells, called vesicles, are much smaller. The cells of the majority of organisms possess a single nucleus, although the cells of fungi and some other groups have several to many nuclei. Most cells derive all of their power from mitochondria, whereas plant cells contain a second kind of bacteria-like powerhouse, chloroplasts, in addition to their mitochondria. As we will see, these differences are relatively minor compared with the many ways in which all cells resemble one another.

So, we can make a conclusion: a cell is a membrane-bound unit containing the DNA hereditary machinery, as well as membranes, organelles, and cytoplasm.

 

CELL SIZE

 Sometimes important things seem so obvious that they are overlooked; when we study cells, for example, it is important that we do not overlook one of their most remarkable traits – their very small size. Cells are not like shoeboxes, big and easy to study. Instead, they are much smaller. Most kinds are so small that you cannot see a single one with the naked eye. Your body contains over 100 trillion cells. If each cell were the size of a shoebox, and lined up end to end, the line would extend to Mars and back, over 500 thousand million kilometers!

 There are about 70 different chemical elements in the living organisms. All of them are devided into four groups:

–                              macroelements (they take 1% and more) – oxygen, hydrogen, carbon, phosphorus, calcium and nitrogen;

–                              oligoelements (0,1-1%) – potassium, sodium, chlorine, sulfur, magnesium and ferrum;

–                              microelements (0,01% and less) – zinc, fluorine, manganese, cobalt, iodine, bromine;

–                              ultramicroelements (their concentration is 10^-4 to 10^-6 %) – aluminium, boran, silicon, cadmium, lithium, selenium etc.

 

The Cell Theory

It is because cells are so small that they were not observed until microscopes were invented in the mid-seventeenth century. Cells were first described by Robert Hooke in 1665, when he used a microscope he had built to examine a thin slice of cork. Hooke observed a honeycomb of tiny empty compartments, similar to that shown in a photograph taken through a microscope of his time. He called the compartments in the cork cellulae, using the Latin word for a small room. His term has come down to us as cells. The first living cells were observed by the Dutch naturalist Antonie van Leeuwenhoek, a few years later, van Leeuwenhoek called the tiny organisms that he observed “animalicules” – little animals. For another century and a half, however, the general importance of cells was not appreciated by biologists. In 1838 Matthias Schleiden, after a careful study of plant tissues, made the first statement of what we now call the cell theory. Schleiden stated that all plants “are aggregates of fully individualized, independent, separate beings, namely the cells themselves.” The following year, Theodor Schwann reported that all animal tissues are also composed of individual cells.

The cell theory, in its modern form, includes the following three principles:

1. All organisms are composed of one or more cells, within which the life processes of metabolism and heredity occur.

2. Cells are the smallest living things, the basic unit of organization of all organisms.

3. Cells arise only by division of a previously existing cell. Although life evolved spontaneously in the hydrogen-rich environment of the early earth, biologists have concluded that additional cells are not originating at present. Rather, life on earth represents a continuous line of descent from those early cells.

The conclusion is: all the organisms on earth are cells or aggregates of cells, and all of us are descendants of the first cells.

 

Cell Walls

Bacteria are encased by a strong cell wall, in which a carbohydrate matrix (a polymer of sugars) is cross-linked by short polypeptide units. No eukaryotes possess cell walls with a chemical composition of this kind. Bacteria are commonly classified as gram-positive and gram-negative by differences in their cell walls. The name refers to the Danish microbiologist Hans Christian Gram, who developed a staining process that distinguishes the two classes of bacteria as a way to detect the presence of certain disease-causing bacteria. Gram-positive bacteria have a single, thick cell wall that retains the Gram stain within the cell, causing the stained cells to appear purple under the microscope. More complex cell walls have evolved in other groups of bacteria. In them, the cell wall is thinner and it does not retain the Gram stain; such bacteria are called gram-negative. Bacteria are often susceptible to different kinds of antibiotics, depending on the structure of their cell walls.

 Simple Interior Organization

 If you were to look at an electron micrograph of a thin section of a bacterial cell, you would be struck by its simple organization. There are few if any internal compartments bounded by membranes and no membrane-bounded organelles – the kinds of distinct structures that are so characteristic of eukaryotic cells. The entire cytoplasm of a bacterial cell is one unit, with no internal support structure; thus the strength of the cell comes primarily from its rigid wall.

The external membrane of bacterial cells often intrudes into the interior of the cell, where it may play an important role. When the cells of bacteria divide, for example, the circular, closed DNA molecule replicates first, and the two DNA molecules that result attach to the cell membrane at different points. Their attachment at different points ensures that the resulting daughter cells will each contain one of the identical units of DNA. In some photosynthetic bacteria, the cell membrane is often extensively folded, with the folds extending into the cell’s interior. These folded membranes are where the bacterial pigments connected with photosynthesis are located.

Since there are no membrane-bounded compartments within a bacterial cell, however, both the DNA and the enzymes within such a cell have access to all parts of the cell. Reactions are not compartmentalized as they are in eukaryotic cells, and the whole bacterium operates very much as a single unit.

So, bacteria are encased by an exterior wall composed of carbohydrates cross-linked by short polypeptides. They lack interior compartments.

A COMPARISON OF BACTERIA AND EUKARYOTIC CELLS

Eukaryotic cells (Figure 1) are far more complex than prokaryotic ones. Compared with their bacterial ancestors, eukaryotic cells exhibit the following significant morphological differences:

1. Their DNA is packaged tightly into compact units containing both DNA and proteins. These units, which are called chromosomes, are located within a separate organelle, the nucleus.

2. The interiors of eukaryotic cells are subdivided into membrane-bounded compartments, which permit one biochemical process to proceed independently of others that may be going on at the same time. The compartmentalization of biochemical activities in eukaryotes serves to increase the efficiency of the various processes.

3. The cells of animals and some protists lack cell walls. Plants possess cell walls, but they are totally different in character from bacterial cell walls: cellulose fibers are embedded in a matrix of other polysaccharides and of protein, producing a strong fiberglass-like structure.

4. No prokaryotes contain internal sacs. By contrast, the mature cells of plants often contain large fluid-filled internal sacs called central vacuoles. Animal cells do not possess such large vacuoles.

So, the interiors of eukaryotic cells are subdivided by membranes in a complex way. The DNA of the cell is present within the nucleus, associated with protein, in units called chromosomes. Most eukaryotes possess cell walls, although cell walls are lacking in animals and some single-celled organisms.

 

Although eukaryotic cells are diverse in form and function, they share a basic architecture. They all are bounded by a membrane called the plasma membrane, they all contain a supporting matrix of protein called a cytoskeleton, and they all possess numerous organelles. The major organelles are of three general kinds: class 1, membrane structures or organelles derived from membranes; class 2, bacteria-like organelles involved in energy production; and class 3, organelles involved in gene expression.

Golgi bodies

lysosomes

microbodies

The membranes of the eukaryotic cell, and the organelles derived from them (class 1), interact as an endomembrane system. All of these endomembranes give rise to one another, are in physical contact with one another, or pass tiny membrane-bound sacs called vesicles to one another. The endomembrane system includes the endoplasmic reticulum, nuclear envelope, Golgi complex, lysosomes, microbodies, and the plasma membrane (which is not really an endomembrane, but is continuous with it).

 

THE ENDOPLASMIC RETICULUM

 When viewed with a light microscope, the interiors of eukaryotic cells exhibit a relatively featureless matrix, within which various organelles are embedded. When viewed with an electron microscope, however, a very striking difference becomes evident – the interiors of eukaryotic cells are seen to be packed with membranes. So thin that they are not visible with the relatively low resolving power of light microscopes, these membranes fill the cell, dividing it into compartments, channeling the transport of molecules through the interior of the cell, and providing the surfaces on which enzymes act. This system of internal compartments created by these membranes in eukaryotic cells constitutes the most fundamental distinction between eukaryotes and prokaryotes.

The extensive system of internal membranes that exists within the cells of eukaryotic organisms is called the endoplasmic reticulum, often abbreviated ER. The term endoplasmic means “within the cytoplasm,” and the term reticulum comes from a Latin word that means “a little net.” Like the plasma membrane, the endoplasmic reticulum is composed of a bilayer of lipid, with various enzymes attached to its surface. The endoplasmic reticulum, weaving in sheets through the interior of the cell, creates a series of channels and interconnections between its membranes that isolates some spaces as membrane-enclosed sacs called vesicles.

 

Rough ER and Ribosomes

 The surface of the endoplasmic reticulum is the place where the cell manufactures proteins intended for export from the cell. Enzymes and protein hormones like insulin are secreted from the cell surface. The manufacture of proteins is carried out by ribosomes, large molecular aggregates of protein and ribonucleic acid (RNA), which translate RNA copies of genes into protein.

Proteins intended for export outside the cell contain special amino acid sequences called signal sequences. As a new protein is made by a free ribosome (one not attached to a membrane), the signal portion of the growing polypeptide attaches a recognition factor that carries the aggregate of genetic message, ribosome, and partially completed protein to a “docking site” on the surface of the endoplasmic reticulum.

When the protein is complete, it passes through the ER membrane into the vesicle-forming system called the Golgi complex (discussed later). It then travels within vesicles to the inner surface of the cell, where it is released outside of the cell in which it was produced. From the time the protein is first attached to the ER it is, in a sense, already located outside the cell.

The surfaces of those regions of the ER devoted to the synthesis of such transported proteins are heavily studded with ribosomes. Their membrane surfaces appear pebbly, like the surface of sandpaper, when viewed with an electron microscope. Because of this “rocky beach” appearance, the regions of ER that are rich in bound ribosomes are often termed rough ER (Figure 7). Regions of the endoplasmic reticulum in which bound ribosomes are relatively scarce are correspondingly called smooth ER.

 

Smooth ER

 Many of the cell’s enzymes cannot function when floating free in the cytoplasm; they are active only when they are associated with a membrane. ER membranes contain many such enzymes embedded within them. Enzymes anchored within the ER, for example, catalyze the synthesis of a variety of carbohydrates and lipids. In cells that carry out extensive lipid synthesis, such as the cells of the testicles, smooth ER is particularly abundant. Intestinal cells, which synthesize triglycerides, and brain cells are also rich in smooth ER. In the liver, enzymes embedded within the smooth ER are involved in a variety of detoxification processes. Drugs such as amphetamines, morphine, codeine, and phenobarbital are detoxified in the liver by components of the smooth ER.

The endoplasmic reticulum (ER) is an extensive system of membranes that divides the interior of eukaryotic cells into compartments and channels. Rough ER synthesizes proteins to be exported, whereas smooth ER organizes the synthesis of lipids and other biosynthetic activities.

 

MICROBODIES

            Eukaryotic cells contain a variety of enzyme-bearing, membrane-bound vesicles called microbodies. Microbodies, thought to be derived from endoplasmic reticulum, are organelles that carry a set of enzymes active in converting fat to carbohydrate, and another set that destroys harmful peroxides. Similar sets of enzymes are found in the microbodies of plants, animals, fungi, and protists, although traditionally animal microbodies are called peroxisomes and plant microbodies are called glyoxysomes. The distribution of enzymes into microbodies is one of the principal ways in which eukaryotic cells organize their metabolism.

Many of the enzymes within microbodies are oxidative enzymes that catalyze the removal of electrons and associated hydrogens. If these enzymes were not isolated within microbodies, they would tend to short-circuit the metabolism of the cytoplasm, much of which involves the addition of hydrogen atoms to oxygen.

The name given to animal microbodies, peroxisomes, refers to the chemical hydrogen peroxide (H₂O₂), which is produced as a by-product of the activities of many of the oxidative enzymes within the microbody. Hydrogen peroxide is a dangerous by-product because it is violently reactive chemically. Microbodies cope with hydrogen peroxide by destroying it; they contain an enzyme catalase, which breaks down the hydrogen peroxide into harmless constituents:

                                      [CATALASE]

                      2 H₂O₂                                2H₂O     +      O₂

                    DROGEN                    WATER      OXYGEN

                   PEROXIDE                                         GAS

 

THE GOLGI COMPLEX

 At various locations within the cytoplasm, flattened stacks of membranes called Golgi bodies occur (Figure 8). These structures are named for Camillo Golgi, the nineteenth century Italian physician who first called attention to them. Animal cells contain 10 to 20 Golgi bodies each (they are especially abundant in glandular cells, which manufacture the substances that they secrete), whereas plant cells may contain several hundred. Collectively the Golgi bodies are referred to as the Golgi complex.

Golgi bodies function in the collection, packaging, and distribution of molecules synthesized in the cell. The proteins and lipids that are manufactured on the rough and smooth ER membranes are transported through the channels of the endoplasmic reticulum, or as vesicles budded off from it, into the Golgi bodies. Within the Golgi bodies, many of these molecules are bound to polysaccharides, forming compound molecules. Among these are glycoproteins, which consist of a polysaccharide complexed to a protein, and glycolipids, consisting of a polysaccharide bound to a lipid. The newly formed glycoproteins and glycolipids collect at the ends of the membranous folds of the Golgi bodies; these folds are given the special name cisternae (Latin, “collecting vessels”). Intermittently in such regions, the membranes of the cisternae push together, pinching off small membrane-bound vesicles containing the glycoprotein and glycolipid molecules. These vesicles then move to other locations in the cell, distributing the newly synthesized molecules within them to their appropriate destinations.

The Golgi complex is the delivery system of the eukaryotic cell. It collects, packages, modifies, and distributes molecules that are synthesized at one location within the cell and used at another.

 

LYSOSOMES

 Lysosomes provide an impressive example of the metabolic compartmentalization achieved by the activity of the Golgi complex. Lysosomes are vesicles that contain a concentration of hydrolytic digestive enzymes, which catalyze the hydrolysis and rapid breakdown of proteins, nucleic acids, lipids, and carbohydrates – in other words, the breakdown of essentially every major macromolecule in the cell.

Lysosomes digest worn-out cellular components, making way for newly formed components while recycling the materials locked up in the old ones. This is perhaps their most important function in the cell. Cells can persist for a long time only if their component parts are constantly renewed. Otherwise the ravages of use and accident chip away at the metabolic capabilities of the cell, slowly degrading its ability to survive. Cells age for the same reason that people do, because of a failure to renew themselves. Lysosomes destroy the organelles of eukaryotic cells and recycle their component proteins and other molecules at a fairly constant rate throughout the life of the cell. Mitochondria, for example, are replaced in some tissues every 10 days, with lysosomes digesting the old mitochondria as new ones are produced.

Lysosomes that are actively engaged in digestive activities keep their battery of hydrolytic enzymes fully active by maintaining a low internal pH – they pump protons into their interiors. Only at such acid pH values are the hydrolytic enzymes maximally active. Lysosomes that are not being used do not maintain such an acid internal pH. A lysosome in such an inactive “holding pattern” is called a primary lysosome. When a primary lysosome fuses with a food vacuole or other organelle, the pH falls and the arsenal of hydrolytic enzymes is activated (a secondary lysosome).

It is not known what prevents lysosomes from digesting themselves, but the process requires energy, which is the reason why metabolically inactive eukaryotic cells die. Without a constant input of energy, the hydrolytic enzymes of primary lysosomes digest the lysosomal membrane from within. When these membranes disintegrate, the digestive enzymes of the lysosomes pour out into the cytoplasm of the cell and destroy it. Bacteria, in contrast, do not possess lysosomes and do not die when they are metabolically inactive. They are simply able to remain quiescent until altered conditions restore their metabolic activity, a property that greatly heightens their ability to persist under unfavorable environmental conditions. For us, the very process that repairs the ravages of time to our cells may also lead to their destruction. An absolute dependency on a constant supply of energy is the price that we pay for our long lives.

In addition to their role in eliminating organelles and other structures within cells, lysosomes also eliminate whole cells. Selective cell death is one of the principal mechanisms used by multicellular organisms in their achievement of complex patterns of development. When a tadpole develops into a frog, the cells of the tail are destroyed by the enzymes from lysosomes. Many cells in your brain die during development, as do the cells of the “tail” you had as an embryo. This directed cellular suicide is accomplished by the rupture of the lysosomes within the cells that are being eliminated. Once released from ruptured lysosomes, the oxidative enzymes proceed to digest the entire cell, a process which is irreversible and quickly leads to cell death.

Lysosomes are vesicles, formed by the Golgi complex, that contain digestive enzymes. The isolation of these enzymes in lysosomes protects the rest of the cell from inappropriate digestive activity.

 

ENERGY-PRODUCING ORGANELLES

 Most of the membrane-bound structures within eukaryotic cells are derived from the endoplasmic reticulum, but there are important exceptions. Eukaryotic cells also contain complex cell-like organelles that most biologists believe were derived from ancient symbiotic bacteria. Symbiosis, the living together in close association of two or more organisms, is one of the most prominent features of life on earth. An organism that is symbiotic within another is called an endosymbiont. The major endosymbionts that occur in eukaryotic cells are mitochondria, which occur in all but a very few eukaryotic organisms, and chloroplasts, which occur in algae and plants.

 

Mitochondria

 Mitochondria are thought by most biologists to have originated as symbiotic, aerobic (oxygen-requiring) bacteria. The theory of the symbiotic origin of mitochondria has had a controversial history, and a few biologists still do not accept it. The evidence supporting the theory is so extensive, however, that we will treat it as established. We will present the evidence as we proceed.

According to this theory, the bacteria that became mitochondria were engulfed by ancestral eukaryotic cells early in their history. Before they had acquired these bacteria, the host cells were unable to carry out the metabolic reactions necessary for living in an atmosphere that contained increasing amounts of oxygen. Reactions requiring oxygen are collectively called oxidative metabolism, a process that the engulfed bacteria were able to carry out. The engulfed bacteria became the inner part of mitochondria.

Mitochondria (singular, mitochondrion) are tubular or sausage-shaped organelles 1 to 3 micrometers long (Figure 10); thus they are about the same size as most bacteria. Mitochondria are bounded by two membranes. The outer membrane is smooth and was apparently derived from the endoplasmic reticulum of the host cell, whereas the inner one is folded into numerous contiguous layers called cristae. These cristae resemble the folded membranes that occur in various groups of bacteria. The cristae partition the mitochondrion into two compartments, an inner matrix and an outer compartment. On the surfaces of the inner membrane, and also submerged within it, are the proteins that carry out oxidative metabolism.

During the billion and a half years in which mitochondria have existed as endosymbionts in eukaryotic cells, most of their genes have been transferred to the chromosomes of their host cells. For example, the genes that produce the enzymes involved with oxidative metabolism, the process that is characteristic of mitochondria, are located in the nucleus. Mitochondria still have their own genome, however, contained within a circular, closed molecule of DNA similar to that found in bacteria. On this mitochondrial DNA are located several genes that produce some of the proteins essential for the role of the mitochondria as the site of oxidative metabolism. All of these genes are copied into RNA within the mitochondrion and used there to make proteins. In this process the mitochondria use small RNA molecules and ribosomal components that are also encoded within the mitochondrial DNA. These ribosomes are smaller than those of eukaryotes in general, resembling bacterial ribosomes in size and structure.

A eukaryotic cell does not produce brand new mitochondria each time the cell itself divides. Instead, the ones it has divide in two, doubling the number, and these are partitioned between the new cells. Thus all mitochondria within a eukaryotic cell are produced by the division of existing mitochondria, just as all bacteria are produced from existing bacteria by cell division. Mitochondria divide by simple fission, splitting in two just as bacterial cells do, and apparently replicate and partition their circular DNA molecule in much the same way as do bacteria. Mitochondrial reproduction is not autonomous (self-governed), however, as is bacterial reproduction. Most of the components required for mitochondrial division are encoded as genes within the eukaryotic nucleus and translated into proteins by the cytoplasmic ribosomes of the cell itself. Mitochondrial replication is thus impossible without nuclear participation, and mitochondria cannot be grown in a cell-free culture.

 

Chloroplasts

 Symbiotic events similar to those postulated for the origin of mitochondria also seem to have been involved in the origin of chloroplasts, which are characteristic of photosynthetic eukaryotes (algae and plants). Chloroplasts, which apparently were derived from symbiotic photosynthetic bacteria, give these eukaryotes the ability to perform photosynthesis. The advantage that chloroplasts bring to the organisms that possess them is therefore obvious: these organisms can manufacture their own food.

So, we can say that mitochondria apparently originated as endosymbiotic aerobic bacteria, whereas chloroplasts seem to have originated as endosymbiotic anaerobic, photosynthetic bacteria.

The chloroplast body is bounded, like the mitochondrion, by two membranes that resemble those of mitochondria (Figure 11) and that apparently were derived in a similar fashion. Chloroplasts are larger than mitochondria, and their inner membranes have a more complex organization. Instead of forming a single isolated compartment within the organelle, as do mitochondrial cristae, the internal chloroplast membranes lie in close association with one another; by fusing along their peripheries, two adjacent membranes form a disk-shaped closed compartment called a thylakoid. On the surface of the thylakoids are the light-capturing photosynthetic pigments. Chloroplasts contain stacks of such thylakoids, which, when viewed with a microscope, resemble stacks of coins. Each stack, called a granum (plural, gratia), may contain from a few to several dozen thylakoids, and a chloroplast may contain a hundred or more grana.

The circular DNA molecule of chloroplasts is larger than that of mitochondria, but many of the genes that specify chloroplast components are located in the nucleus, so that the transfer of genetic material has been a part of their history also. Some components of the photosynthetic process are synthesized entirely within the chloroplast, which includes the specific RNA and protein components necessary to accomplish this. Photosynthetic cells typically contain from one to several hundred chloroplasts, depending on the organism involved or, in the case of multicellular photosynthetic organisms, the kind of cell.

Most green plants can synthesize chlorophyll only in the presence of light. In the dark the production of chlorophyll ceases, and in many plants most of the lamellae are reabsorbed. When reabsorption occurs, the chloroplast, largely devoid of internal membrane invaginations, is called a leucoplast. In the root cells and various storage cells of plants, leucoplasts may serve as sites of storage for starch. A leucoplast that stores starch is sometimes termed an amyloplast. Many plant pigments other than chlorophyll likewise occur in chloroplasts. A collective term for these different kinds of organelles, all derived from chloroplasts, is plastid. Like mitochondria, all plastids come from the division of existing plastids.

So, we can arrive at the conclusion that both mitochondria and chloroplasts have lost the bulk of their genomes to the host chromosomes, but retain certain specific genes related to their functions. Neither kind of organelle can be maintained in a cell-free culture.

 

THE CYTOSKELETON

            The cytoplasm of all eukaryotic cells is crisscrossed by a network of protein fibers, which support the shape of the cell and anchors organelles such as the nucleus to fixed locations (Figure 12). This network, called the cytoskeleton, cannot be seen with an ordinary microscope because the fibers are single chains of protein, much too fine for microscopes to resolve. The fibers of the cytoskeleton are a dynamic system, constantly being formed and disassembled. Individual fibers form by polymerization, a process in which identical protein subunits are attracted to one another chemically and spontaneously assemble into long chains. Fibers are disassembled in the same way, by the removal of first one subunit, then another from one end of the chain.

Cells from plants and animals contain the following three different types of cytoskeleton fibers, each formed from a different kind of subunit (Figure 13):

1. Actin filaments. Actin filaments (also called microfilaments) are long protein fibers about 7 nanometers in diameter, each fiber composed of two chains of protein loosely twined around one another like two strands of pearls. Each “pearl” of a filament is a ball-shaped molecule of a protein called actin, the size of a small enzyme. Actin molecules left alone will spontaneously form these filaments, even in a test tube; a cell regulates the rate of their formation by means of other proteins that act as switches, turning on polymerization only when appropriate.

2. Microtubules. Microtubules are hollow tubes about 25 nanometers in diameter, each a chain of proteins wrapped round and round in a tight spiral. The basic protein subunit of a microtubule is a molecule a little larger than actin, called tubulin. Like actin filaments, microtubules form spontaneously, but in a cell microtubules form only around specialized structures called organizing centers, which provide a base from which they can grow.

3. Intermediate filaments. The most durable element of the cytoskeleton is a system of tough protein fibers, each a rope of threadlike protein molecules wrapped around one another like the strands of a cable. These fibers are characteristically 8 to 10 nanometers in diameter, intermediate in size between actin filaments and microtubules; this is why they are called intermediate filaments. Once formed, intermediate filaments are very stable and do not usually break down. The most common basic protein subunit of an intermediate filament is called vimentin, although some cells employ other fibrous proteins instead. Skin cells, for example, form intermediate filaments from a protein called keratin. When skin cells die, the intermediate filaments of their cytoskeleton persist – hair and nails are formed in this way.

Both actin filaments and intermediate filaments are anchored to proteins embedded within the plasma membrane and provide the cell with mechanical support. Intermediate filaments act as intracellular tendons, preventing excessive stretching of cells, whereas actin filaments play a major role in determining the shape of cells. Because actin filaments can form and dissolve so readily, the shape of an animal cell can change quickly. If you look at the surface of an animal cell under a microscope, you will find it alive with motion, projections shooting outward from the surface and then retracting, only to shoot out elsewhere moments later (Figure 14).

Not only is the cytoskeleton responsible for the cell’s shape, but it also provides a scaffold on which the enzymes and other macromolecules are located in defined areas of the cytoplasm. Many of the enzymes involved in cell metabolism, for example, bind to actin filaments, as do ribosomes that carry out protein synthesis. By anchoring particular enzymes near one another, the cytoskeleton serves, like the endoplasmic reticulum, to organize the cell’s activities.

Actin filaments and microtubules also play important roles in cell movement. Pairs of microtubules are cross-linked at numerous positions by molecules of protein. The shifting positions of these cross-links determine the relative motion of the microtubules. As an example of the results of microtubule movement, when we study cell reproduction, we will see that chromosomes move to opposite sides of dividing cells because they are attached to shortening microtubules, and that the cell pinches into two because a belt of actin filaments contracts like a purse-string. Your own muscle cells utilize actin filaments to contract their cytoskeletons. Indeed, all cell motion is tied to these same processes. The fluttering of an eyelash, the flight of an eagle, the awkward crawling of a baby, all depend on the movements of actin filaments in the cytoskeletons of muscle cells.

 FLAGELLA

 

            Flagella (singular, ftagellum) are fine, long, threadlike organelles protruding from the surface of cells; they are used in locomotion and feeding. The flagella of bacteria are long protein fibers, which are so efficient that the bacteria that possess them can move about 20 cell diameters per second. Imagine trying to run 20 body lengths per second! The bacteria swim by rotating their flagella (Figure 15). One or more flagella trail behind each swimming bacterial cell, depending on the species of bacterium. Each has a motion like a propeller, caused by a complex rotary “motor” embedded within the cell wall and membrane. This rotary motion is virtually unique to bacteria; only a very few eukaryotes have organs that truly rotate.

 There are two fundamental types of cells according to presence or absence of a nucleus: prokaryotic and eukaryotic.

 

Difference between Prokaryotic and Eukaryotic cells

 

 

The main components of eukaryotic cell are: 1) Cell membrane (is also known as plasma membrane, plasmalemma); 2) Nucleus; 3) Cytoplasm.

1.                       Plasma membrane envelops the cell and aids in maintaining its structural and functional integrity. It is composed of a lipid bilayer and assosiated proteins. Lipid bilayer is composed by phospholipids (hydrophilic heads and hydrophobic tails), glycolipids and cholesterol. Membrane proteins may be integral, which dissolved in the lipid bilayer and peripheral proteins, which don’t extend into the lipid bilayer. They may be divided into three groups: channel-forming proteins, receptors and markers. On an outside surface of plasma membrane (in animal cells) there is glycocalyx. It consists of glycoproteins and glycolipids.

 

The functions of plasma membrane (semipermeable membrane between the cytoplasm and the extracellular environment) are: passage of water, passage of bulb material (phagocytosis and pinocytosis), selective transport of molecules, reception of information, expression of cell identity, physical connection with other cells, enzyme activity.

2. Nucleus consists of nuclear envelope, nucleolus, nucleoplasm and chromatin (chromosomes). Nuclear envelope surrounds the nuclear material, consists of two parallel membranes separated from each other by a narrow perinuclear space. Nuclear envelope is perforated at intervals by openings called nuclear pores.

Nucleolus is a well-defined nuclear inclusion (sometime more than one). It is present in the cells that actively synthesize proteins. They become detectable only when the cell is in interphase. It is involved in the synthesis of rRNA.

Nucleoplasm is the portion of the protoplasm that is surrounded by the nuclear envelope. It consists of a matrix and various types of particles.

Chromatin is double-stranded DNA complexed with histones and acidic proteins. It is responsible for RNA synthesis, resides within the nucleus in two forms: heterochromatin and euchromatin.

 

The main  functions of the nucleus are: 1) direct protein synthesis in the cytoplasm via ribosomal ribonucleic acid (rRNA), messenger RNA (mRNA) and transfer RNA (tRNA), which are synthesized in the nucleus; 2) nucleus contains the genetic apparatus encoded in the deoxyribonucleic acid (DNA) of chromosomes.

3. Structural components of the cytoplasm are: 1) cytoskeleton; 2) organelles; 3) inclusions. The fluid component is called cytosol.

The cytoplasm is dynamic functional interactions among certain organelles that result in the uptake and release of material by the cell, protein synthesis and intracellular digestion.

Cytoskeleton is the structural framework within the cytosol. Cytosceleton functions are: to maintain the cell shape, to stabilize the  cell attachments, to facilitate endocytosis and exocytosis, to promote the cell motility. Cytosceleton includes such components as microtubules, microfilaments, intermediate filaments, microtrabecular lattice.

Organelles are the complex of the cells contain specialized structures, which are metabolically active units of living matter and usually are limited by a membrane. They divide into two groups: 1) for general purpose – ribosomes, Rough Endoplasmic reticulum (RER), Smooth Endoplasmic reticulum (SER), annulate lamella, Golgi apparatus, lisosomes, mitochondria, centrosome, vacuoles; 2) for special purpose – myofibrils, cilia and flagella.

Structure and functions of organelles for general purpose

 

 

 

 

 

 

 

Organelles for special purpose characterized for cells that perform special function. They are:

1) myofibrils in muscles tissue;

2)  cilia – thousands of short hair-like structures on the cell surface for movement. Cilia can have different functions: to sweep fluid and particles across the stationary cell. In cells that line the human lungs, for example, cilia sweep dusts particles out toward the air passages to eventually be expelled in mucus or swallowed.

3)  flagella – tail-like single appendage,  which enable the cell to move, f.e. sperm.

       Inclusions are the “lifeless” accumulations of material that are not metabolically active and usually are present in the cytosol only temporarily. They divide into three groups: 1) trophic  (lipid droplets, glycogen, protein); 2) secretary (pancreas secret); 3) special – in high developed cells (hemoglobin in erythrocyte).

 

The Structure and Life Cycle of HIV

How does HIV evade the immune system so efficiently? Why are so many variants of the virus found in a single patient? Understanding the structure and life cycle of the virus is key to answering these questions and essential to the design of effective treatments.

 

 

The structure of HIV

HIV is an enveloped RNA virus: As HIV buds out of the host cell during replication, it acquires a phospholipid envelope. Protruding from the envelope are peg-like structures that the viral RNA encodes. Each peg consists of three or four gp41 glycoproteins (the stem), capped with three or four gp120glycoproteins. Inside the envelope the bullet-shaped nucleocapsid of the virus is composed of protein, and surrounds two single strands of RNA. Three enzymes important to the virus’s life cycle – reverse transcriptase, integrase, and protease – are also within the nucleocapsid.

Although helper T cells seem to be the main target for HIV, other cells can become infected as well. These include monocytes and macrophages, which can hold large numbers of viruses within themselves without being killed. Some T cells harbor similar reservoirs of the virus. 

Entry of HIV into the host cell requires the binding of one or more gp120 molecules on the virus to CD4 molecules on the host cell’s surface. Binding to a second receptor is also required. Ed Berger helped identify this coreceptor. As he compared his results with those of other researchers, it became clear that two different coreceptors are involved in the binding. One, CCR5, achemokine receptor, serves as a coreceptor early in an infection. Another chemokine receptor (CXCR4) later serves as a coreceptor. That two coreceptors are involved is consistent with previous observations. Viruses isolated from individuals early in an infection, during the asymptomatic phase, will typically infect macrophages in the laboratory, but not T cells (the viruses are M-tropic). Virus isolated from patients later in the infection in the symptomatic phase, will infect T cells (the viruses are T-tropic). It seems that a shift takes place in the viral population during the progression of the infection, so that new cellular receptors are used and different cells become infected. 
         HIV is a member of the group of viruses known as retroviruses, which share a unique life cycle. Once HIV binds to a host cell, the viral envelope fuses with the cell membrane, and the virus’s RNA and enzymes enter the cytoplasm. HIV, like other retroviruses, contains an enzyme called reverse transcriptase. This allows the single-stranded RNA of the virus to be copied and double-stranded DNA (dsDNA) to be generated. The enzyme integrase then facilitates the integration of this viral DNA into the cellular chromosome.Provirus (HIV DNA) is replicated along with the chromosome when the cell divides. The integration of provirus into the host DNA provides the latency that enables the virus to evade host responses so effectively. 

Production of viral proteins and RNA takes place when the provirus is transcribed. Viral proteins are then assembled using the host cell’s protein-making machinery. The virus’s protease enzyme allows for the processing of newly translated polypeptides into the proteins, which are then ultimately assembled into viral particles. The virus eventually buds out of the cell. A cell infected with a retrovirus does not necessarily lyse the cell when viral replication takes place; rather, many viral particles can bud out of a cell over the course of time.

HIV Transmission

HIV is transmitted principally in three ways: by sexual contact, by blood (through transfusion, blood products, or contaminated needles), or by passage from mother to child. Although homosexual contact remains a major source of HIV within the United States, “heterosexual transmission is the most important means of HIV spread worldwide today.” ² Treatment of blood products and donor screening has essentially eliminated the risk of HIV from contaminated blood products in developed countries, but its spread continues among intravenous drug users who share needles. In developing countries, contaminated blood and contaminated needles remain important means of infection. Thirteen to thirty-five percent of pregnant women infected with HIV will pass the infection on to their babies; transmission occurs in utero, as well as during birth. Breast milk from infected mothers has been shown to contain high levels of the virus also. HIV is not spread by the fecal-oral route; aerosols; insects; or casual contact, such as sharing household items or hugging. The risk to health care workers is primarily from direct inoculation by needle sticks. Although saliva can contain small quantities of the virus, the virus cannot be spread by kissing.

2.                       Cell membranes. Transport of substances through plasmalema

1. Fluid-mosaic model of the plasma membrane.

1.1. Lipid component.

1.2.          Protein component.

1.3.          Glycocalyx.

2. Function of plasmalemma.

3.     Movement of molecules into and out of cells.

3.1. Diffusion.

3.2. Osmosis.

3.3. Tonicity.

3.4. Transport by carriers.

3.5. Active transport. Structure and function of ATP.

3.6. Endocytosis and exocytosis.

4. Receptors of the cells.

5. Junctions between cells.

 

 The plasma membrane is about 7.5 nanometers (nm) thick and consists of a lipid bilayer and associated proteins.The inner leaflet of the plasma membrane faces the cytoplasm and the outer leaflet faces the extracellular environment. The plasma membrane displays a trilaminar (unit membrane) structure when examined by transmission electron microscopy (ТЕМ).

          Function:

1.  The plasma membrane envelops the cell and maintains its structural and functional integrity.

2.   It acts as a semipermeable membrane between the cytoplasm and the external environment.

3.  It permits the cell to recognize (and be recognized by) other cells and macromolecules.

     Fluid mosaic model of the plasma membrane.

     The lipid bilayer is composed of phospholipids, glycolipids, and cholesterol. Phospholipids consist of one hydrophillic head and two hydrophobic fatty acyl tails. Glycolipids are restricted to the outer leaflet. Polar carbohydrate residues of glycolipids extend from the outer leaflet into the extracellu­lar space and form part of the glycocalyx. Cholesterol constitutes 2% of plasmalemma lipids, is present in both leaflets, and helps to maintain the structural integrity of the membrane. Fluidity of the lipid bilayer is crucial to exocytosis, endocytosis, membrane trafficking, and membrane biogenesis.

       Membrane proteins include integral proteins and peripheral proteins. Integral proteins are dissolved in the lipid bilayer. Transmembrane proteins span the entire plasma membrane and function as membrane receptors and transport proteins. Most transmembrane proteins are glycoproteins. Transmembrane proteins are amphipathic and contain hydrophilic and hydrophobic amino acids, some of them interact with the hydrocarbon tails of the membrane phospholipids.

     Peripheral proteins do not extend into the lipid bilayer. These proteins are located on the cytoplasmic aspect of the inner leaflet. The outer leaflets of some cells possess covalently linked glycolipids to which peripheral proteins are anchored; thus these peripheral proteins project into the extracellular space. Peripheral proteins bond to the phospholipid polar groups or integral proteins of the membrane via noncovalent interactions. They usually function as a part of the cytoskeleton or as a part of an intracellular second messenger system.

     The lipid-to-protein ratio in plasma membranes ranges from 1:1 (by weight) in most cells to 4:1 in myelin.

     Glycocalyx (cell coat) is the sugar coat located on the outer surface of the outer leaflet of the plasmalemma. When it is examined by ТЕМ, it varies in appearance (fuzziness) and thickness (up to 50 nm).

  Function. 1) The glycocalyx aids in attachment of cells (e.g., fibroblasts but not epithelial cells) to extracellular matrix components. 2) It binds antigens and enzymes to the cell surface. 3) It facilitates cell-cell recognition and interaction.

       Plasma Membrane Transport Processes. These processes include transport of a single molecule (uniport) or cotransport of two different mole­cules in the same (symport) or opposite (antiport) direction.

 

       Passive transport includes simple and facilitated diffusion.

Neither of these processes requires energy because molecules move across the plasma membrane down a concentration or electrochemical gradient.

1.  Simple diffusion transports small nonpolar molecules (e.g., 0₂ and N₂) and small, uncharged, polar molecules (e.g., H₂0, C0₂, and glycerol). It exhibits little specificity, and the diffusion rate is proportional to the concen­tration gradient of the diffusing molecule.

2.  Facilitated diffusion occurs via ion channel and/or carrier proteins, structures that exhibit specificity for the transported molecules. It is faster than simple diffusion; ions and large polar molecules are thus capable of traversing membranes that would otherwise be impermeable to them.

a. Ion channel proteins are highly folded transmembrane proteins that form small aqueous pores across membranes through which specific small water-soluble molecules and ions pass down an electrochemical gradient.

b. Carrier proteins are highly folded transmembrane proteins that un­dergo reversible conformational change, thus transporting specific mole­cules across the membrane; these proteins function in both passive transport and active transport.

3. Osmosis is the diffusion of water across a selectively permeable membrane in response to its concentration gradient.

a. When solute concentrations are equal on both sides of a cell membrane, there is no net movement of water in either direction; the two fluids are said to be isotonic (“iso-“ means same).

b. When solute concentrations are not equal, one fluid is hypotonic (has fewer solutes) and the other is hypertonic (has more solutes). Because water moves down its concentration gradient, it tends to move from a hypotonic solution to a hypertonic one.

Active transport is an energy-requiring process which transports a molecule against an electrochemical gradient via carrier proteins.

Na⁺-K⁺ pump  mechanism. The Na⁺-K⁺ pump involves the antiport transport of Na⁺ and K⁺ ions mediated by the carrier protein, Na⁺-K⁺ ATPase. Na⁺ ions are pumped out of the cell and two K⁺ ions are pumped into the cell. The hydrolysis of a single ATP molecule by the Na⁺-K⁺ ATPase is required to transport five ions.

        ATP (adenosine triphosphate) – is the common energy currency of cells; when cells require energy, they “spend” ATP. ATP production occurs at the cristae of mitochondria. The average male needs to produce about 8 kJ of ATP an hour. ATP is a nucleotide composed of the base adenine and the sugar ribose (together they are called adenosine) and 3 phosphate groups. Function of ATP: 1) Chemical function. It supplies the energy needed to synthesize macromolecules that make up the cell. 2) Transport function. It supplies the energy needed to pump substances across the plasma membrane. 3) Mechanical function. It supplies the energy needed to cause muscles to contract, cilia and flagella to beat, chromosomes to move etc. All organisms use ATP. It illustrates the chemical unity of all living things.

        Endocytosis and exocytosis are ways that substances can enter and exit cells. Part of the plasma membrane pinches off and forms small membrane-bound sacs, or vesicles, around some substance. Vesicles are formed even around tiny cells (such as a bacteria) and fluids. During exocytosis, vesicles are formed inside the cytoplasm and then move to the plasma membrane and are fused with it, so their content is transferred outside. During endocytosis, a patch of plasma membrane encloses material at the cell surface. Then it sinks in and pinches off, forming a vesicle that either transports the material into the cytoplasm or stores it there. Phagocytosis (cell eating) is transport process by which amoeboid-type cells engulf large material, forming an intracellular vacuole. When macromolecules are taken in by endocytosis, the process is called pinocytosis (cell drinking), and the result is formation of vesicle. Both phagocytic vacuoles and pinocytic vesicles can fuse with lysosomes, whose enzymes digest their contents.

 

 

 

Endocytosis pathways could be subdivided into four categories: namely, clathrin-mediated endocytosis, caveolae, macropinocytosis, and phagocytosis.

·         Clathrin-mediated endocytosis is mediated by small (approx. 100 nm in diameter) vesicles that have a morphologically characteristic crystalline coat made up of a complex of proteins that are mainly associated with the cytosolic protein clathrin. Clathrin-coated vesicles (CCVs) are found in virtually all cells and form domains of the plasma membrane termed clathrin-coated pits. Coated pits can concentrate large extracellular molecules that have different receptors responsible for the receptor-mediated endocytosis of ligands, e.g. low density lipoprotein, transferrin,growth factors, antibodies and many others.

·         Caveolae are the most common reported non-clathrin-coated plasma membrane buds, which exist on the surface of many, but not all cell types. They consist of the cholesterol-binding protein caveolin (Vip21) with a bilayer enriched in cholesterol and glycolipids. Caveolae are small (approx. 50 nm in diameter) flask-shape pits in the membrane that resemble the shape of a cave (hence the name caveolae). They can constitute up to a third of the plasma membrane area of the cells of some tissues, being especially abundant in smooth muscle, type Ipneumocytes, fibroblasts, adipocytes, and endothelial cells. Uptake of extracellular molecules is also believed to be specifically mediated via receptors in caveolae.

·         Macropinocytosis, which usually occurs from highly ruffled regions of the plasma membrane, is the invagination of the cell membrane to form a pocket, which then pinches off into the cell to form a vesicle (0.5–5 µm in diameter) filled with a large volume of extracellular fluid and molecules within it (equivalent to ~100 CCVs). The filling of the pocket occurs in a non-specific manner. The vesicle then travels into the cytosol and fuses with other vesicles such as endosomes and lysosomes.

·         Phagocytosis is the process by which cells bind and internalize particulate matter larger than around 0.75 µm in diameter, such as small-sized dust particles, cell debris, micro-organismsand even apoptotic cells, which only occurs in specialized cells. These processes involve the uptake of larger membrane areas than clathrin-mediated endocytosis and caveolae pathway.

More recent experiments have suggested that these morphological descriptions of endocytic events may be inadequate, and a more appropriate method of classification may be based upon the clathrin-dependence of particular pathways, with multiple subtypes of clathrin-dependent and clathrin-independent endocytosis. Mechanistic insight into non-phagocytic, clathrin-independent endocytosis has been lacking, but a recent study has shown how Graf1 regulates a highly prevalent clathrin-independent endocytic pathway known as the CLIC/GEEC pathway.

Exocytosis (ɛksoʊsaɪˈtoʊsɪs/; from Greek ἔξω “out” and English cyto- “cell” from Gk. κύτος “receptacle”) is the durable, energy-consuming process by which a cell directs the contents of secretory vesicles out of the cell membrane and into the extracellular space. These membrane-bound vesicles contain soluble proteins to be secreted to the extracellular environment, as well as membrane proteinsand lipids that are sent to become components of the cell membrane. However, the mechanism of the secretion of intravesicular contents out of the cell is very different from the incorporation in the cell membrane of ion channels, signaling molecules, or receptors. While for membrane recycling and the incorporation in the cell membrane of ion channels, signaling molecules, or receptors complete membrane merger is required, for cell secretion there is transient vesicle fusion with the porosome at the cell membrane in a process called exocytosis, dumping its contents out of the cell’s environment. Examination of cells following secretion using electron microscopy, demonstrate increased presence of partially empty vesicles following secretion. This suggested that during the secretory process, only a portion of the vesicular content is able to exit the cell. This could only be possible if the vesicle were to temporarily establish continuity with the cell plasma membrane, expel a portion of its contents, then detach, reseal, and withdraw into the cytosol (endocytose). In this way, the secretory vesicle could be reused for subsequent rounds of exo-endocytosis, until completely empty of its contents.^[1]

Certain vesicle-trafficking steps require the transportation of a vesicle over a moderately small distance. For example, vesicles that have the duty to transport the proteins from the Golgi apparatusto the cell surface area, will be likely to use motor proteins and a cytoskeletal track to get closer than previously stated to their target. Before tethering would have been appropriate, many of the proteins used for the active transport would have been instead set for passive transport, due to the fact that the Golgi apparatus does not require ATP to transport proteins. Both the actin- and the microtubule-base are implicated in these processes, along with several motor proteins. Once the vesicles reach their targets, they come into contact with tethering factors that can restrain them.

Vesicle tethering

It is useful to distinguish between the initial, loose tethering of vesicles with their objective from the more stable, packing interactions. Tethering involves links over distances of more than about half the diameter of a vesicle from a given membrane surface (>25 nm). Tethering interactions are likely to be involved in concentrating synaptic vesicles at the synapse.

The vesicles are also involved in regular cell’s transcription processes.

Vesicle docking

Secretory vesicles transiently dock at the cell plasma membrane, preceding the formation of a tight t-/v-SNARE complex, leading to priming and the establishment of continuity between the opposing bilayers.

Vesicle priming

Ieuronal exocytosis, the term priming has been used to include all of the molecular rearrangements and ATP-dependent protein and lipid modifications that take place after initial docking of a synaptic vesicle but before exocytosis, such that the influx of calcium ions is all that is needed to trigger nearly instantaneous neurotransmitter release. In other cell types, whose secretion is constitutive (i.e. continuous, calcium ion independent, non-triggered) there is no priming.

Vesicle fusion

Further information: Vesicle fusion

Transient vesicle fusion is driven by SNARE proteins, resulting in release of vesicle contents into the extracellular space (or in case of neurons in the synaptic cleft).

The merging of the donor and the acceptor membranes accomplishes three tasks:

·         The surface of the plasma membrane increases (by the surface of the fused vesicle). This is important for the regulation of cell size, e.g., during cell growth.

·         The substances within the vesicle are released into the exterior. These might be waste products or toxins, or signaling molecules like hormones or neurotransmitters during synaptic transmission.

·         Proteins embedded in the vesicle membrane are now part of the plasma membrane. The side of the protein that was facing the inside of the vesicle now faces the outside of the cell. This mechanism is important for the regulation of transmembrane and transporters.

 Receptor-mediated endocytic cycle is a form of pinocytosis that is very specific because it involves the use of plasma membrane receptors. A macromolecule that binds to a receptor is called a ligand. The binding of ligands to specific receptor sites causes the receptors to gather at one location before endocytosis occurs. This location is called a coated pit because there is a layer of fibrous protein, called clathrin, on the cytoplasmic side. Clathrin is a protein designed to form lattices around membranous vesicles. When a vesicle forms, it also is coated, but soon it loses its coat. At this point the ligands can directly enter the cell or else end up in lysosomes, which digest them to smaller molecules, which enter the cell. In any case, the receptors return to the plasma membrane and exocytosis occurs. The importance of receptor-mediated endocytosis is ex­emplified by the occurrence of a genetic disease. Normally cells take up cholesterol, which is carried in the blood by a lipoprotein called low density lipoprotein (LDL). When cells need more cholesterol for membrane production they produce receptors for LDL. After LDL molecules bind to receptors, receptor-mediated endocytosis occurs. Later, the receptors are returned to the plasma membrane and lysosomes disengage cholesterol from LDL. This whole process goes awry in individuals who lack a gene or inherit a faulty gene for the LDL receptor. Because cholesterol is unable to enter their cells, it builds up and forms plaque on blood vessel walls leading to cardiovascular disease and heart attacks. Children with this genetic disorder have been known to have heart attacks even as early as 6 years old.