cell membrane - the thin layer of protein and fat that surrounds the cell.

The cell membrane is semipermeable, allowing some substances to pass into the cell and blocking others. centrosome - (also called the "microtubule organizing center") a small body located near the nucleus - it has a dense center and radiating tubules. The centrosomes is where microtubules are made. During cell division (mitosis), the centrosome divides and the two parts move to opposite sides of the dividing cell. The centriole is the dense center of the centrosome. cytoplasm - the jellylike material outside the cell nucleus in which the organelles are located. Golgi body - (also called the Golgi apparatus or golgi complex) a flattened, layered, sac-like organelle that looks like a stack of pancakes and is located near the nucleus. It produces the membranes that surround the lysosomes. The Golgi body packages proteins and carbohydrates into membrane-bound vesicles for "export" from the cell. lysosome - (also called cell vesicles) round organelles surrounded by a membrane and containing digestive enzymes. This is where the digestion of cell nutrients takes place. mitochondrion - spherical to rod-shaped organelles with a double membrane. The inner membrane is infolded many times, forming a series of projections (called cristae). The mitochondrion converts the energy stored in glucose into ATP (adenosine triphosphate) for the cell. nuclear membrane - the membrane that surrounds the nucleus. nucleolus - an organelle within the nucleus - it is where ribosomal RNA is produced. Some cells have more than one nucleolus. nucleus - spherical body containing many organelles, including the nucleolus. The nucleus controls many of the functions of the cell (by controlling protein synthesis) and contains DNA (in chromosomes). The nucleus is surrounded by the nuclear membrane. ribosome - small organelles composed of RNA-rich cytoplasmic granules that are sites of protein synthesis. rough endoplasmic reticulum - (rough ER) a vast system of interconnected, membranous, infolded and convoluted sacks that are located in the cell's cytoplasm (the ER is continuous with the outer nuclear membrane). Rough ER is covered with ribosomes that give it a rough appearance. Rough ER transports materials through the cell and produces proteins in sacks called cisternae (which are sent to the Golgi body, or inserted into the cell membrane). smooth endoplasmic reticulum - (smooth ER) a vast system of interconnected, membranous, infolded and convoluted tubes that are located in the cell's cytoplasm (the ER is continuous with the outer nuclear membrane). The space within the ER is called the ER lumen. Smooth ER transports materials through the cell. It contains enzymes and produces and digests lipids (fats) and membrane proteins; smooth ER buds off from rough ER, moving the newly-made proteins and lipids to the Golgi body, lysosomes, and membranes. vacuole - fluid-filled, membrane-surrounded cavities inside a cell. The vacuole fills with food being digested and waste material that is on its way out of the cell.

amyloplast - an organelle in some plant cells that stores starch. Amyloplasts are found in starchy plants like tubers and fruits. ATP - ATP is short for adenosine triphosphate; it is a highenergy molecule used for energy storage by organisms. In plant cells, ATP is produced in the cristae of mitochondria andchloroplasts.

cell membrane - the thin layer of protein and fat that surrounds the cell, but is inside the cell wall. The cell membrane is semipermeable, allowing some substances to pass into the cell and blocking others. cell wall - a thick, rigid membrane that surrounds a plant cell. This layer of cellulose fiber gives the cell most of its support and structure. The cell wall also bonds with other cell walls to form the structure of the plant. centrosome - (also called the "microtubule organizing center") a small body located near the nucleus - it has a dense center and radiating tubules. The centrosomes is where microtubules are made. During cell division (mitosis), the centrosome divides and the two parts move to opposite sides of the dividing cell. Unlike the centrosomes in animal cells, plant cell centrosomes do not have centrioles. chlorophyll - chlorophyll is a molecule that can use light energy from sunlight to turn water and carbon dioxide gas into sugar and oxygen (this process is called photosynthesis). Chlorophyll is magnesium based and is usually green. chloroplast - an elongated or disc-shaped organelle containing chlorophyll. Photosynthesis (in which energy from sunlight is converted into chemical energy - food) takes place in the chloroplasts. christae - (singular crista) the multiply-folded inner membrane of a cell's mitochondrion that are finger-like projections. The walls of the cristae are the site of the cell's energy production (it is where ATP is generated). cytoplasm - the jellylike material outside the cell nucleus in which the organelles are located. Golgi body - (also called the golgi apparatus or golgi complex) a flattened, layered, sac-like organelle that looks like a stack of pancakes and is located near the nucleus. The golgi body packages proteins and carbohydrates into membrane-bound vesicles for "export" from the cell. granum - (plural grana) A stack of thylakoid disks within the chloroplast is called a granum. mitochondrion - spherical to rod-shaped organelles with a double membrane. The inner membrane is infolded many times, forming a series of projections (called cristae). The mitochondrion converts the energy stored in glucose into ATP (adenosine triphosphate) for the cell. nuclear membrane - the membrane that surrounds the nucleus. nucleolus - an organelle within the nucleus - it is where ribosomal RNA is produced. nucleus - spherical body containing many organelles, including the nucleolus. The nucleus controls many of the functions of the cell (by controlling protein synthesis) and contains DNA (in chromosomes). The nucleus is surrounded by the nuclear membrane photosynthesis - a process in which plants convert sunlight, water, and carbon dioxide into food energy (sugars and starches), oxygen and water. Chlorophyll or closely-related pigments (substances that color the plant) are essential to the photosynthetic process. ribosome - small organelles composed of RNA-rich cytoplasmic granules that are sites of protein synthesis. rough endoplasmic reticulum - (rough ER) a vast system of interconnected, membranous, infolded and convoluted sacks that are located in the cell's cytoplasm (the ER is continuous with the outer nuclear membrane). Rough ER is covered with ribosomes that give it a rough appearance. Rough ER transport materials through the cell and produces proteins in sacks called cisternae (which are sent to the Golgi body, or inserted into the cell membrane). smooth endoplasmic reticulum - (smooth ER) a vast system of interconnected, membranous, infolded and convoluted tubes that are located in the cell's cytoplasm (the ER is continuous with the outer nuclear membrane). The space within the ER is called the ER lumen. Smooth ER transport materials through the cell. It contains enzymes and produces and digests lipids (fats) and membrane proteins; smooth ER buds off from rough ER, moving the newly-made proteins and lipids to the Golgi body and membranes

stroma - part of the chloroplasts in plant cells, located within the inner membrane of chloroplasts, between the grana. thylakoid disk - thylakoid disks are disk-shaped membrane structures in chloroplasts that contain chlorophyll. Chloroplasts are made up of stacks of thylakoid disks; a stack of thylakoid disks is called a granum. Photosynthesis (the production of ATP molecules from sunlight) takes place on thylakoid disks. vacuole - a large, membrane-bound space within a plant cell that is filled with fluid. Most plant cells have a single vacuole that takes up much of the cell. It helps maintain the shape of the cell.

Procaryotic structural components consist of macromolecules such as DNA, RNA, proteins, polysaccharides, phospholipids, or some combination thereof. The macromolecules are made up of primary subunits such as nucleotides, amino acids and sugars (Table 1). It is the sequence in which the subunits are put together in the macromolecule, called the primary structure, that determines many of the properties that the macromolecule will have. Thus, the genetic code is determined by specific nuleotide base sequences in chromosomal DNA; the amino acid sequence in a protein determines the properties and function of the protein; and sequence of sugars in bacterial lipopolysaccharides determines unique cell wall properties for pathogens. The primary structure of a macromolecule will drive its function, and differences within the primary structure of biological macromolecules accounts for the immense diversity of life.

Function(s) Structure Flagella Pili Sex pilus Common pili or fimbriae Capsules (includes "slime layers" and glycocalyx) Cell wall Gram-positive bacteria Prevents osmotic lysis of cell protoplast and confers rigidity and shape on cells Peptidoglycan prevents osmotic lysis and confers rigidity and shape; outer membrane is permeability barrier; associated LPS and proteins have various functions Swimming movement

Predominant chemical composition Protein

Stabilizes mating bacteria during DNA Protein transfer by conjugation Attachment to surfaces; protection against phagotrophic engulfment Attachment to surfaces; protection against phagocytic engulfment, occasionally killing or digestion; reserve of nutrients or protection against desiccation Protein

Usually polysaccharide; occasionally polypeptide

Peptidoglycan (murein) complexed with teichoic acids Peptidoglycan (murein) surrounded by phospholipid protein-lipopolysaccharide "outer membrane"

Gram-negative bacteria

Plasma membrane Ribosomes Inclusions

Permeability barrier; transport of solutes; energy generation; location of Phospholipid and protein numerous enzyme systems Sites of translation (protein synthesis) RNA and protein Highly variable; Often reserves of nutrients; additional carbohydrate, lipid, protein specialized functions or inorganic

Chromosome Plasmid

Genetic material of cell Extrachromosomal genetic material

DNA DNA

Nucleus

The nucleus is one part of a yeast cell, reports History for Kids. The nucleus of a yeast cell is made up of the lipid envelope of the cell and also the DNA molecule that is protected by this lipid envelope. A lipid envelope consists of big, hydrocarbon molecules, and it prevents the yeast cell's DNA molecule from getting damaged or broken in any way. To fit all the DNA into the yeast cell, a spiral shape termed a helix is formed. Vacuoles

Vacuoles are another part of a yeast cell, according to History for Kids. These parts of a yeast cell are defined as small pockets in the cell's cytoplasm that are used to store food for the cell. Cytoplasm is a thick liquid that is found in the cell membrane; it holds the yeast cell's organelles. The composition of vacuoles is primarily amino acids and water. Since the cell's cytoplasm has salty water, vacuoles have a lipid membrane that works to keep this salty water out.

Endoplasmic Reticulum

The endoplasmic reticulum is comprised of a lipid membrane, which is similar to the composition of the cell membrane around a yeast cell, according to History for Kids. The endoplasmic reticulum of a yeast cell evolved approximately two billion years ago from the cell membrane around the cell's nucleus. "Endoplasmic" is a word that represents how the reticulum is floating around in the cell's cytoplasm. "Reticulum" is Latin for net. Thus, the endoplasmic reticulum is a small net that floats around in the yeast cell's cytoplasm. Lysosomes Lysosomes in a yeast cell began their evolution in the cell about two billion years ago. Lysosomes are known as tiny and round bubbles of lipid membrane, indicates History for Kids. The purpose of these lysosomes is to retain hydrogen molecules inside of them; these hydrogen molecules aid in breaking up bigger molecules into smaller ones. This process is basically the digestion of the food of the yeast cell, as well as the breaking up and recycling of garbage and poison in the cell. Lysosomes are known to break down captured bacteria and viruses inside the yeast cell that could destroy it.

Viruses display a wide diversity of shapes and sizes, called morphologies. In general, viruses are much smaller than bacteria. Most viruses that have been studied have a diameter between 20 and 300 nanometres. Some filoviruses have a [61] total length of up to 1400 nm; their diameters are only about 80 nm. Most viruses cannot be seen with an optical [62] microscope so scanning and transmission electron microscopes are used to visualise virions. To increase the contrast between viruses and the background, electron-dense "stains" are used. These are solutions of salts of heavy metals, such astungsten, that scatter the electrons from regions covered with the stain. When virions are coated with stain (positive [63] staining), fine detail is obscured.Negative staining overcomes this problem by staining the background only. A complete virus particle, known as a virion, consists of nucleic acid surrounded by a protective coat of protein called [64] a capsid. These are formed from identical protein subunits called capsomeres. Viruses can have a lipid "envelope" derived from the host cell membrane. The capsid is made from proteins encoded by the viral genome and its shape [65][66] serves as the basis for morphological distinction. Virally coded protein subunits will self-assemble to form a capsid, in general requiring the presence of the virus genome. Complex viruses code for proteins that assist in the construction of

their capsid. Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral nucleic acid is called a nucleocapsid. The capsid and entire virus structure can be mechanically [67][68] (physically) probed through atomic force microscopy. In general, there are four main morphological virus types:

Structure of tobacco mosaic virus:RNA coiled in a helix of repeating protein sub-units

Electron micrograph of icosahedraladenovirus

Herpes viruses have a lipid envelope

Helical These viruses are composed of a single type of capsomer stacked around a central axis to form a helical structure, which may have a central cavity, or hollow tube. This arrangement results in rod-shaped or filamentous virions: These can be short and highly rigid, or long and very flexible. The genetic material, in general, singlestranded RNA, but ssDNA in some cases, is bound into the protein helix by interactions between the negatively charged nucleic acid and positive charges on the protein. Overall, the length of a helical capsid is related to the length of the nucleic acid contained within it and the diameter is dependent on the size and arrangement of capsomers. The well-studied tobacco mosaic virus is an example of a helical virus. Icosahedral Most animal viruses are icosahedral or near-spherical with icosahedral symmetry. A regular icosahedron is the optimum way of forming a closed shell from identical sub-units. The minimum number of identical capsomers required is twelve, each composed of five identical sub-units. Many viruses, such as rotavirus, have more than twelve capsomers and appear spherical but they retain this symmetry. Capsomers at the apices are surrounded by five other capsomers and are called pentons. Capsomers on the triangular faces are surrounded by six others and are called hexons.
[70] [69]

Hexons are in essence flat and pentons, which form the 12 vertices, are curved. The

same protein may act as the subunit of both the pentamers and hexamers or they may be composed of different proteins. Prolate

This is an isosahedron elongated along the fivefold axis and is a common arrangement of the heads of bacteriophages. This structure is composed of a cylinder with a cap at either end. Envelope Some species of virus envelop themselves in a modified form of one of the cell membranes, either the outer membrane surrounding an infected host cell or internal membranes such as nuclear membrane or endoplasmic reticulum, thus gaining an outer lipid bilayer known as a viral envelope. This membrane is studded with proteins coded for by the viral genome and host genome; the lipid membrane itself and any carbohydrates present originate entirely from the host. The influenza virus and HIV use this strategy. Most enveloped viruses are dependent on the envelope for their infectivity. Complex These viruses possess a capsid that is neither purely helical nor purely icosahedral, and that may possess extra structures such as protein tails or a complex outer wall. Some bacteriophages, such as Enterobacteria phage T4, have a complex structure consisting of an icosahedral head bound to a helical tail, which may have a hexagonal base plate with protruding protein tail fibres. This tail structure acts like a molecular syringe, attaching to the bacterial host and then injecting the viral genome into the cell.
[73] [72] [71]

The poxviruses are large, complex viruses that have an unusual morphology. The viral genome is associated with proteins within a central disk structure known as a nucleoid. The nucleoid is surrounded by a membrane and two lateral bodies of unknown function. The virus has an outer envelope with a thick layer of protein studded over its surface. The whole virion is [74] slightly pleiomorphic, ranging from ovoid to brick shape. Mimivirus is the largest characterised virus, with a capsid diameter of 400 nm. Protein filaments measuring 100 nm project from the surface. The capsid appears hexagonal under an electron microscope, therefore the capsid is [75] probably icosahedral. In 2011, researchers discovered a larger virus on ocean floor of the coast of Las Cruces, Chile. Provisionally named Megavirus chilensis, it can be seen with a basic optical [76] microscope. Some viruses that infect Archaea have complex structures that are unrelated to any other form of virus, with a wide variety of unusual shapes, ranging from spindle-shaped structures, to viruses that resemble hooked rods, teardrops or even bottles. Other archaeal viruses resemble the tailed [77] bacteriophages, and can have multiple tail structures.

The Biosphere: Life on Earth Life! It's everywhere on Earth; you can find living organisms from the poles to the equator, from the bottom of the sea to several miles in the air, from freezing waters to dry valleys to undersea thermal vents to groundwater thousands of feet below the Earth's surface. Over the last 3.7 billion years or so, living organisms on the Earth have diversified and adapted to almost every environment imaginable. The diversity of life is truly amazing, but all living organisms do share certain similarities. All living organisms can replicate, and the replicator molecule is DNA. As well, all living organisms contain some means of converting the information stored in DNA into products used to build cellular machinery from fats, proteins, and carbohydrates. Three Domains of Life Click on a domain to begin exploring.

Until comparatively recently, living organisms were divided into two kingdoms: animal and vegetable, or the Animalia and the Plantae. In the 19th century, evidence began to accumulate that these were insufficient to express the diversity of life, and various schemes were proposed with three, four, or more kingdoms. The scheme most often used currently divides all living organisms into five kingdoms: Monera (bacteria), Protista, Fungi, Plantae, and Animalia. This coexisted with a scheme dividing life into two main divisions: the Prokaryotae (bacteria, etc.) and the Eukaryotae (animals, plants, fungi, and protists). Recent work, however, has shown that what were once called "prokaryotes" are far more diverse than anyone had suspected. The Prokaryotae are now divided into two domains, the Bacteria and the Archaea, as different from each other as either is from the Eukaryota, or eukaryotes. No one of these groups is ancestral to the others, and each shares certain features with the others as well as having unique characteristics of its own.

Within the last two decades, a great deal of additional work has been done to resolve relationships within the Eukaryota. It now appears that most of the biological diversity of eukaryotes lies among the protists, and many scientists feel it is just as inappropriate to lump all protists into a single kingdom as it was to group all prokaryotes. Although many revised systems have been proposed, no single one of them has yet gained a wide acceptance. A fourth group of biological entities, the viruses, are not organisms in the same sense that eukaryotes, archaeans, and bacteria are. However, they are of considerable biological importance. The Earth is 4.6 billion years old and microbial life is thought to have first appeared between 3.8 and 3.9 billion years ago; in fact, 80% of Earth's history was exclusively microbial life. Microbial life is still the dominant life form on Earth. It has been estimated that the total number of microbial cells on Earth on the order of 2.5 X 30 10 cells, making it the major fraction of biomass on the planet. Phylogeny refers to the evolutionary relationships between organisms. The Three Domain System, proposed by Woese and others, is an evolutionary model of phylogeny based on differences in the sequences of nucleotides in the cell's ribosomal RNAs (rRNA), as well as the cell's membrane lipid structure and its sensitivity to antibiotics. Comparing rRNA structure is especially useful. Because rRNA molecules throughout nature carry out the same function, their structure changes very little over time. Therefore similarities and dissimilarities in rRNA nucleotide sequences are a good indication of how related or unrelated different cells and organisms are.

There are various hypotheses as to the origin of prokaryotic and eukaryotic cells. Because all cells are similar in nature, it is generally thought that all cells came from a common ancestor cell termed the last universal common ancestor (LUCA). These LUCAs eventually evolved into three different cell types, each representing a domain. The three domains are the Archaea, the Bacteria, and the Eukarya. More recently various fusion hypotheses have begun to dominate the literature. One proposes that the diploid or 2N nature of the eukaryotic genome occurred after the fusion of two haploid or 1N prokaryotic cells. Others propose that the domains Archaea and Eukarya emerged from a common archaeal-eukaryotic ancestor that itself emerged from a member of the domain Bacteria. Some of the evidence behind this hypothesis is based on a "superphylum" of bacteria called PVC, members of which share some characteristics with both archaea and eukaryotes. In any event, it is accepted today that there are three distinct domains of organisms in nature: Bacteria, Archaea, and Eukarya. A description of the three domains follows: 1. The Archaea (archaebacteria) The Archaea possess the following characteristics: Archaea are prokaryotic cells. Unlike the Bacteria and the Eukarya, the Archaea have membranes composed of branched hydrocarbon chains (many also containing rings within the hydrocarbon chains)attached to glycerol by ether linkages (see Fig. 1). The cell walls of Archaea contain no peptidoglycan. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are sensitive to some antibiotics that affect the Eukarya. Archaea contain rRNA that is unique to the Archaea as indicated by the presence molecular regions distinctly different from the rRNA of Bacteria and Eukarya.

Archaea often live in extreme environments and include methanogens, extreme halophiles, and hyperthermophiles. One reason for this is that the ether-containing linkages in theArchaea membranes is more stabile than the ester-containing linkages in the Bacteria and Eukarya and are better able to withstand higher temperatures and stronger acid concentrations. 2. The Bacteria (eubacteria) The Bacteria possess the following characteristics: Bacteria are prokaryotic cells. Like the Eukarya, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages (see Fig. 1). The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain peptidoglycan. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to most antibiotics that affect Eukarya. Bacteria contain rRNA that is unique to the Bacteria as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Eukarya.

Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-negative bacteria. 3. The Eukarya (eukaryotes) The Eukarya (also spelled Eucarya) possess the following characteristics: Eukarya have eukaryotic cells. Like the Bacteria, they have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages (see Fig. 1). Not all Eukarya possess cells with a cell wall, but for those Eukarya having a cell wall, that wall contains no peptidoglycan.

Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to most antibiotics that affect eukaryotic cells. Eukarya contain rRNA that is unique to the Eukarya as indicated by the presence molecular regions distinctly different from the rRNA of Archaea and Bacteria.

The Eukarya are subdivided into the following kingdoms: a. Protista Kingdom Protista are simple, predominately unicellular eukaryotic organisms. Examples includes slime molds, euglenoids, algae, and protozoans. b. Fungi Kingdom Fungi are unicellular or multicellular organisms with eukaryotic cell types. The cells have cell walls but are not organized into tissues. They do not carry out photosynthesis and obtain nutrients through absorption. Examples include sac fungi, club fungi, yeasts, and molds. c. Plantae Kingdom Plants are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and have cell walls. They obtain nutrients by photosynthesis and absorption. Examples include mosses, ferns, conifers, and flowering plants. d. Animalia Kingdom Animals are multicellular organisms composed of eukaryotic cells. The cells are organized into tissues and lack cell walls. They do not carry out photosynthesis and obtain nutrients primarily by ingestion. Examples include sponges, worms, insects, and vertebrates.

It used to be thought that the changes that allow microorganisms to adapt to new environments or alter their virulence capabilities was a relatively slow process occuring within an organism primarily through mutations, chromosomal rearrangements, gene deletions and gene duplications. Those changes would then be passed on to that microbes progeny and natural selection would occur. This gene transfer from a parent organism to its offspring is called vertical gene transmission (def). It is now known that microbial genes are transferred not only vertically from a parent organism to its progeny, but also horizontally to relatives that are only distantly related, eg, other species and other genera. This latter process is known as horizontal gene transfer. Through mechanisms such as transformation, transduction, and conjugation, genetic elements such as plasmids (def), transposons (def), integrons (def), and even chromosomal DNA can readily be spread from one microorganism to another. As a result, the old three-branched "tree of life" in regard to microorganisms now appears to be more of a "net of life." Microbes are known to live in remarkably diverse environments, many of which are extremely harsh. This amazing and rapid adaptability is a result of their ability to quickly modify their repertoire of protein functions by modifying, gaining, or losing their genes.