cell biology and terms....

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THE DISCOVERY OF CELLS
Antony Van Leeuwenhoek built this simple microscope over three hundred years ago. He used it to discover single celled organisms swimming around in pond water.
What Leeuwenhoek imagined, was that the tiny organisms he observed were actually little animals. He called them his “cavorting wee beasties”. He even recorded their means of reproducing. They duplicated their structures and then pulled apart to create two identical individuals.
This kind of reproduction is quite different than having babies or growing a new plant from a seed. In these microscopic organisms one individual duplicates itself becoming identical twin sisters.Around the same time Leeuwenhoek was observing his “wee beasties,” a British scientist, Robert Hook, was turning his more elaborate microscope onto a shaving of cork, just to see if it had a hidden structure of some kind.
He saw that the cork was made up of thousands of little compartments. They reminded him of the prison cells where prisoners were held. Thus the term — cell.

CELL STRUCTURES


Around a hundred years ago microscopes showed that all cells have a common structure. All have an outer membrane that holds the cell together, a membrane that allows some substances to pass, but excludes others.
The cells of plants, animals and “protists” as Leeuwenhoek’s wee beasties came to be called, all contain a nucleus. It was soon realized that this structure somehow controlled the cell’s activities.
The nucleus was seen to duplicate just before cell division, suggesting that it carried hereditary information from one generation of cells to the next.
In cells undergoing division the nucleus broke down and its internal structures became visible -- chromosomes

Each species has a characteristic chromosome number. Humans have 23 pairs of chromosomes in each of their body cells.
Outside of the nucleus is a soupy fluid containing many small bodies, a cell’s organs, and appropriately called organelles.
In a cell that has been squeezed by the cover glass to the point of rupture, a bubble forms. In this bubble you can clearly see the tiny cell organelles called mitochondria.
Similar organelles were eventually found in all cells, both plant, animal and protist.
Mitochondria were eventually isolated and their function was discovered. They are the bodies where sugars and other food molecules are metabolized, with the help of oxygen, to supply energy for cell use – the process of cellular respiration.
Plants and green protists have an additional cell organelle clearly visible: rounded green bodies called chloroplasts.
These green bodies are where photosynthesis occurs.
In the process of photosynthesis chloroplasts use the energy in light to convert carbon dioxide from the air into sugars and other organic compounds needed by the plant


Cells - Structure and Function

Important Events in the Discovery of Cells

• 1665 - Robert Hooke looks at cork under a microscope. Calls the chambers he see "cells"
• 1665 - 75 Anton van Leeuwenhoek, the person incorrectly given credit for the invention of the microscope (actually, he was just damn good at making and using them, and his scopes soon became the standard, and history has just given him credit as the inventor of the microscope), studies organisms living in pond water (like you did in lab). He calls them "Animalcules."
• 1830 - German scientists Schleiden and Schawann summarize the findings of many scientists and conclude that all living organisms are made of cells. This forms the basis of the Cell Theory of Biology

The Cell Theory of Biology

• All organisms are composed of cells
• The cell is the structural unit of life - units smaller than cells are not alive
• Cells arise by division of preexisting cells - spontaneous generation does not exist
• Cells can be cultured to produce more cells
  • in vitro = outside organism or cell
  • in vivo = inside organism or cell

Properties of Cells


Cells are complex and highly organized

• They contain numerous internal structures
• Some are membrane bound (organelles) while others do not

Cells contain a genetic blueprint and machinery to use it

• Genes are instructions for cells to create specific proteins
• All cells use the same types of information
  • The genetic code is universal
  • The machinery used for synthesis is interchangeable
• However, for this to function properly, information transfer must be error free
  • Errors are called mutations

Cells arise from the division of other cells

• Daughter cells inherit the genes from the mother cells
• Binary fission - cell division in bacteria
• Mitosis - the genetic complement of each daughter cell is identical to the other and to the mother cell. This is asexual reproduction
• Meiosis - the genetic complement of each daughter cell is reduced by half and each daughter cell is genetically unique. This is used in sexual reproduction
• Daughter cells inherit cytoplasm and organelles from the mother cells
  • Asexual - organelles from mother cell
  • Sexual - organelles predominately from one parent
    • In eukaryotes, the chloroplasts and mitochondria come from the egg cell
    • This can be used to trace the evolutionary origin of the organism

Cells acquire and utilize energy

• Plant cells undergo photosynthesis
  • convert light energy and CO2 to chemical energy (ATP and glucose)
• Most cells respire
  • release energy found in organic compounds
  • convert organic compounds to CO2 and O2
  • make ATP

Cells can perform a variety of chemical reactions

• Transform simple organic molecules into complex molecules (anabolism)
• Breakdown complex molecules to release energy (catabolism)
• Metabolism = all reactions performed by cells

Cells can engage in mechanical activities

• Cells can move
• Organelles can move
• Cells can respond to stimuli
  • chemotaxis - movement towards chemicals
  • phototaxis - movement towards light
  • hormone responses
  • touch responses

Cells can regulate activities

• Cells control DNA synthesis and cell division
• Gene regulation - cells make specific proteins only when needed
• Turn on and off metabolic pathways

Cells all contain the following structures:

• Plasma membrane - separates the cell from the external environment
• Cytoplasm - fluid-filled cell interior
• Nuclear material - genetic information stored as DNA

Types of Cells

Prokaryotes

• Pro = before; karyon = nucleus
• relatively small - 5 to 10 um
• lack membrane-bound organelles
• earliest cell type

Archaea

• Originally thought to be prokaryotes
• relatively small - 5 to 10 um
• lack membrane-bound organelles
• Usually live in extreme environments (thermophiles, halophiles, etc)

Eukaryotes

• Eu = true; karyon = nucleus
• contain membrane-bound organelles
• Evolved from prokaryotes by endosymbiotic association of two or more prokaryotes
• Include Protists, Fungi, Animals, and Plants

Features of Prokaryotic Cells

• Capsule - outer sticky protective layer
• Cell Wall - rigid structure which helps the bacterium maintain its shape
  • this is in NO way the same as the cell wall of a plant cell
• Plasma membrane - separates the cell from the environment
• Mesosome - infolding of plasma membrane to aid in compartmentalization
• Nucleoid - region where nakedDNA is found
• Cytoplasm
  • semi-fluid cell interior
  • no membrane-bound organelles
  • location for metabolic enzymes
  • location of ribosomes for protein synthesis

Properties of Eukaryotic Cells

A Typical Plant Cell

A Typical Animal Cell

• Eukaryotic features shared with Prokaryotic cells
  • Rigid cell wall
    • Plant cells, some Fungi, some Protists
    • Animal cells lack cell wall
    • bacterial and eukaryotic cell walls are analogous structures
  • Plasma membrane
  • Cytoplasm with ribosomes
  • Nuclear material

• Cytoskeleton - flexible tubular scaffold of microfilaments
  • maintains cell shape and provides support
  • anchors organelles & enzymes to specific regions of the cell
  • contractility and movement (amoeboid movement)
  • intracellular transport - tracks for vesicle and organelle movement by motor proteins
• Cytoskeleton components
  • Microfilaments
    • solid protein (actin) which is assembled at one end and disassembled at the other end
    • actin filaments can change lenght - a process known as treadmilling
    • actin frequently interacts with myosin, a second protein capable of movement - like in your muscles
  • Intermediate filaments
    • rope-like fibrous proteins - defined by size, not by composition like microfilaments and microtubules
    • provide structural reinforcement
    • anchor organelles
    • keep nucleus in place
  • Microtubules
    • hollow tubes of tubulin (a globular protein)
    • maintains cell shape
    • anchor organelles
    • movement of organelles
    • track for motor proteins such as kinesin
• Cilia and Flagella - involved in cellular movement
  • composed of microtubules
  • cilia - short, numerous, complex
  • flagella - longer, fewer, less complex
  • both arranged in a 9+2 pattern with dynein arms projecting outward
  • Movement is through associations with dynein, a motor protein similar to myosin and kinesin
• Nucleus
  • Double membrane with pores
  • Outer membrane continuous with ER (therefore part of the endomembrane system)
  • Nuclear matrix - protein-containing fibrilar network
  • Nucleoplasm - the fluid substance in which the solutes of the nucleus are dissolved
  • Chromosomes - histone protein and DNA complexes
    • heterochromatin - highly compact, supercoiled chromatin
    • euchromatin - long, filamentous strands of chromatin (gene transcription?)
  • Nucleolus - involved in the synthesis and assembly of ribosomes
• Endomembrane System
  • Endoplasmic Reticulum - an extensive membranous network continuous with the outer nuclear membrane.
    • Rough ER - has ribosomes associated with it and is involved in secreted protein synthesis
    • Smooth ER - lacks ribosomes and is involved in membrane lipid synthesis
  • Golgi Apparatus
    • Flattened vesicles in stacks which receive protein from ER
    • Form secretory vesicles to transport proteins to different parts of the cell (vacuole, lysosome, etc) or for secretion
    • cis face - "receiving" side of Golgi apparatus
    • trans face - "shipping" side of Golgi apparatus
  • Lysosome
    • lysosomes are special types of vacuoles
    • contain enzymes for use in the hydrolytic breakdown of macromolecules
    • Three ways to enter a lysosome - phagocytosis, autophagy, and receptor-mediated endocytosis
• Peroxisome
  • Eukaryotic organelle that degrades fatty acids and amino acids
  • Also degrades the resulting hydrogen peroxide
  • There is a variety of different types of peroxisomes, each which breaks down different type of molecules
• Plant Central Vacuole - major storage space in center of plant cell with many functions
  • Digestive - break down of macromolecules
  • Storage - ions, sugars, amino acids, toxic waste
  • Maintain cell rigidity - high ionic concentration generates high water potential

• Transport of Proteins - the ER, Golgi, and transport vesicles
  • Ribosomes (see below) synthesize proteins
    • Those destines for secretion contain a short sequence of amino acids that interact with a receptor protein on the surface of rough ER
    • The ribosome interacts with the receptor protein, causing the synthesized protein to enter the ER
    • The receptor protein removes the signal sequence
  • Proteins that enter the ER are usually glycolated
    • The carbohydrate groups serve as chemical markers for protein distribution
    • The carbohydrate groups can be modified within the ER
  • In the Golgi Apparatus, proteins are segregated for transport to other regions in the cell
    • The sugars attached to proteins bind to receptors in the trans walls of the Golgi
    • These walls eventually bud off into the cytoplasm
    • The vesicles then bind to the appropriate endomembrane system (ER, plasma membrane, etc) and release the contents.

Images of Vesicle Transport Between Endomembrane Organelles

• Ribosomes
  • Technically not an organelle, since there is no membrane, but they are prominent cellular structures and usually lumped in with the organelles
  • The "factories" of the cell - involved in protein synthesis
  • Facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis
  • May either be free or bound to ER
  • Made up of two subunits, the large and the small subunit
  • Both subunits are constructed out of protein and RNA (called rRNA)
  • The ribosomes of prokaryotes and eukaryotes vary slightly with regard to size and shape

• Mitochondria
  • Found in ALL eukaryotic cells (yes, even in plant cells)
  • Site of aerobic respiration
    • sugars + O2 - - > ATP + CO2 + H2O
  • Contain DNA which codes for mitochondrial proteins, ribosomes, etc.
  • Divide by a process similar to binary fission when cell divides
  • Enclosed in a double membrane system
    • Inner Membrane forms the Cristae (invaginations into interior region)
      • Site of energy generation
    • Matrix is the soluble portion of the mitochondria
      • Site of carbon metabolism
      • Location of mDNA
      • Site of mitochondrial protein synthesis
• Chloroplasts
  • Found only in plant cells
  • Site of photosynthesis
    • conversion of solar energy to chemical energy in the form of ATP and sugars
  • Contain DNA which codes for chloroplast proteins, ribosomes, etc.
  • Divide when plant cell divides
  • Enclosed in a double membrane envelope that does not invaginate into the chloroplast
  • Thylakoid is a third internal membrane system
    • contains membrane-bound photosynthetic pigments
    • site of photochemistry (the conversion of light energy to ATP)
    • site of O2 generation
  • Stroma is soluble portion of chloroplast
    • site of CO2 fixation
    • site of sugar synthesis (carbon metabolism)
    • location of cpDNA
    • site of chloroplast protein synthesis

Endosymbiotic Origin of Chloroplasts and Mitochondria

• Free-living prokaryote eaten by host
• Genes transferred to host nucleus
• Some genes retained but most lost - can no longer survive outside of host
• Symbiotic relationship
  • photosynthetic symbiont provides sugar - degenerates to form chloroplast
  • aerobic symbiont provides a more efficient energy generation system - degenerates to form mitochondria
  • host provides stable environment, nutrients, energy, and most proteins
• Evidence for Endosymbiotic Theory
  • Chloroplasts and mitochondria have DNA
    • does not code for all proteins
    • some genes in nucleus
    • proteins imported rom cytoplasm
  • Organelle proteins similar to bacterial form
  • Ribosome structure and metabolic enzymes more similar to bacterial forms

CELL FUNCTION AND STRUCTURE

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Muscle cell
Muscle is a contractiletissue of animals and is derived from the mesodermal layer of embryonic germ cells. Muscle cells contain contractile filaments that move past each other and change the size of the cell. They are classified as skeletal, cardiac, or smooth muscles. Their function is to produce force and cause motion. Muscles can cause either locomotion of the organism itself or movement of internal organs. Cardiac and smooth muscle contraction occurs without conscious thought and is necessary for survival. Examples are the contraction of the heart and peristalsis which pushes food through the digestive system. Voluntary contraction of the skeletal muscles is used to move the body and can be finely controlled. Examples are movements of the eye, or gross movements like the quadriceps muscle of the thigh. There are two broad types of voluntary muscle fibers: slow twitch and fast twitch. Slow twitch fibers contract for long periods of time but with little force while fast twitch fibers contract quickly and powerfully but fatigue very rapidly.



Muscle cells are individual cells that comprise the muscle tissue of the body and execute muscle contraction. There are three types of muscle cells: skeletal, cardiac, and smooth. Each of these types differ in cellular structure, specific function, and location within the body. Together, the three muscle cell types play specific roles in supporting the skeletal structure and posture of the body, assisting in the flow of blood through blood vessels, aiding in digestion, and driving the heartbeat.
Skeletal muscle cells are found throughout the body, making up skeletal muscle that is anchored to the bones by ligaments. During development, skeletal muscle cells are made from precursor cells, called myoblasts, which fuse together to form long, cylindrical, mature muscle cells. Each muscle cell contains several nuclei — one from each myoblast that is used to make up the cell — and fibers that have striations where the myoblasts were fused together. Skeletal muscle cells allow for muscle contraction, and they are responsible for movement and the upright posture of the body. These cells are voluntary muscle cells, meaning they receive signals from the brain to perform contraction.

Cardiac muscle cells are found in the walls of the heart. Like skeletal muscle cells, mature cardiac muscle cells have a striated appearance, which is a result of different protein fibers within the cardiac muscle cell. Each cardiac muscle cell has a number of irregular branches, and each branch is connected to branches on neighbor cells by an adhering structure called an intercalated disc. Cardiac muscle cells are highly resistant to fatigue, and their regular contraction allows for beating of the heart, thereby pumping blood out of the heart and into the blood vessels. These cells are said to be involuntary, since they do not rely on conscious signals from the brain to contract.
Smooth muscle is structurally distinct from skeletal and cardiac muscle cells. Unlike these cell types, a smooth muscle cell does not have a striated appearance, and instead forms homogeneous bundles. Smooth muscle cells are found in a number of systems throughout the body; for example, they make up a component of veins and arteries, and surround organs in the gastrointestinal tract.
A layer of smooth muscle cells surrounds veins and arteries to provide strength and aid in movement of blood through the vessel. Smooth muscle cells also surround the esophagus, stomach, small intestines, and large intestines to aid in digestion and movement of food through the digestive system. Like cardiac muscle cells, contraction of a smooth muscle cell is involuntary and does not require conscious signals from the brain to contract and perform its functions throughout the body.

Anatomy of a muscle cell

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Bacteria

Bacteria are microscopic organisms whose single cells have neither a membrane-enclosed nucleus nor other membrane-enclosed organelles like mitochondria and chloroplasts. Another group of microbes, the archaea, meet these criteria but are so different from the bacteria in other ways that they must have had a long, independent evolutionary history since close to the dawn of life. In fact, there is considerable evidence that you are more closely related to the archaea than they are to the bacteria.

Properties of Bacteria

• prokaryotic (no membrane-enclosed nucleus)
• no mitochondria or chloroplasts
• a single chromosome
  • a closed circle of double-stranded DNA
  • with no associated histones
• If flagella are present, they are made of a single filament of the protein flagellin; there are none of the "9+2" tubulin-containing microtubules of the eukaryotes.
• ribosomes differ in their structure from those of eukaryotes [More]
• have a rigid cell wall made of peptidoglycan.
• The plasma membrane (in Gram-positive bacteria) and both membranes in Gram-negative bacteria are phospholipid bilayers but contain no cholesterol or other steroids.
• no mitosis
• mostly asexual reproduction
• any sexual reproduction very different from that of eukaryotes; no meiosis
• Many bacteria form a single spore when their food supply runs low. Most of the water is removed from the spore and metabolism ceases. Spores are so resistant to adverse conditions of dryness and temperature that they may remain viable even after 50 years of dormancy.

Classification of Bacteria

Until recently classification has done on the basis of such traits as:

• shape
  • bacilli: rod-shaped
  • cocci: spherical
  • spirilla: curved walls
• ability to form spores
• method of energy production (glycolysis for anaerobes, cellular respiration for aerobes)
• nutritional requirements
• reaction to the Gram stain.

Gram-positive bacteria are encased in a plasma membrane covered with a thick wall of peptidoglycan. Gram-negative bacteria are encased in a triple-layer. The outermost layer contains lipopolysaccharide (LPS). The Gram stain is named after the 19th century Danish bacteriologist who developed it.

• The bacterial cells are first stained with a purple dye called crystal violet.
• Then the preparation is treated with alcohol or acetone.
• This washes the stain out of Gram-negative cells.
• To see them now requires the use of a counterstain of a different color (e.g., the pink of safranin).
• Bacteria that are not decolorized by the alcohol/acetone wash are Gram-positive.

Although the Gram stain might seem an arbitrary criterion to use in bacterial taxonomy, it does, in fact, distinguish between two fundamentally different kinds of bacterial cell walls and reflects a natural division among the bacteria.
More recently, genome sequencing, especially of their 16S ribosomal RNA (rRNA), has provided additional insights into the evolutionary relationships among the bacteria.
Firmicutes

Comparison of their sequenced genomes reveals that all the Gram-positive rods and cocci as well as the mycoplasmas belong to a single clade that has been named the Firmicutes.
Gram-Positive Rods

Aerobic Gram-Positive Rods

• Bacillus anthracis/cereus/thuringiensis. These organisms differ mainly in the plasmids they contain.
  • B. anthracis causes anthrax. Currently the biological agent favored by terrorists. Its 2 plasmids contain the genes needed to synthesize
    • a capsule which (like those of pneumococci) makes it resistant to phagocytosis, and
    • the three components of the toxin that causes the disease symptoms. [More]
  • B. thuringiensis — the organism, its toxin, and even the gene (also plasmid-encoded) for the toxin are used as biocontrol agents against a variety of insect pests. [Link to discussion]
• Bacillus subtilis. A common soil bacterium. Its chromosome contains 4,214,814 bp of DNA encoding 4,100 genes.
• Lactobacillus. Several species are used to convert milk into cheese, butter, and yogurt.

Anaerobic Gram-Positive Rods:

• Clostridium tetani. Clostridia are spore-forming obligate anaerobes. The spores of C. tetani are widespread in the soil and often get into the body through wounds. Puncture wounds (e.g., by splinters or nails) are particularly dangerous because they provide the anaerobic conditions needed for germination of the spores and growth of the bacteria. C. tetani liberates a toxin that blocks transmitter release (by destroying the SNAREs needed) at inhibitory synapses in the spinal cord and brain. This interferes with the reciprocal inhibition of antagonistic pairs of skeletal muscles so the victim suffers violent muscle spasms. Fortunately, the disease — called tetanus — is now rare in developed countries, thanks to almost universal immunization against the toxin. Chemical alteration of the toxin produces a toxoid that still retains the epitopes of the toxin. Incorporated in a vaccine, the toxoid provides a relatively long-lasting (~10 years) immunity against tetanus.
• Clostridium botulinum. As little as 1 µg of its toxin eaten with an uncooked bean or mushroom can be fatal. The toxin blocks the release of acetylcholine (also by destroying the SNAREs needed for exocytosis) from the terminals of motor neurons. Thus the victim shows signs of sympathetic nervous activity (dilation of the pupils, inhibition of urination) and skeletal muscle weakness. If the intercostal muscles are effected, breathing may stop. The toxin is a protein and is quickly (10 minutes) denatured at 100 °C, so boiling home-canned products makes them safe to eat.

Gram-Positive Cocci

The bacteria in this group grow in characteristic colonies.

• Staphylococci form flat packets of cells. Two species are common:
  • Staphylococcus albus is probably growing right now on your skin.
  • Staphylococcus aureus is also a frequent inhabitant of the skin, nasal passages, and the gastrointestinal tract. It can cause acne and, if it gets under the skin, abscesses. In hospitals, the development of antibiotic resistant S. aureus has become a major problem. Some strains of Staphylococcus aureus secrete a toxin and can cause life-threatening toxic shock syndrome.
  Many cases of "food poisoning" are caused by staphylococci.
• Most Streptococci grow in chains. The electron micrograph (courtesy of the Naval Dental Research Institute, Great Lakes, IL) shows Streptococcus mutans, a common inhabitant of the mouth. Streptococci cause
  • "strep throat"
  • impetigo
  • middle ear infections
  • scarlet fever (a result of a toxin produced by the organism)
  • rheumatic fever
  • a rare form of toxic shock syndrome
• Pneumococci. The cells of these streptococci grow in pairs. Streptococcus pneumoniae causes bacterial pneumonia. This was once a major killer — especially of the aged and infirm — but today there is an effective vaccine and any infections that do occur usually respond quickly to antibiotics.

Mycoplasmas

Mycoplasmas have the distinction of being the smallest living organisms. They are so small (0.1 µm) that they can be seen only under the electron microscope.
Mycoplasmas are obligate parasites; that is, they can live only within the cells of other organisms. They are probably the descendants of Gram-positive bacteria who have lost their peptidoglycan wall as well as much of their genome — now depending on the gene products of their host.
The DNA sequences of the complete genomes of seven mycoplasmas have been determined, including

• Mycoplasma genitalium has 580,073 base pairs of DNA encoding 517 genes (480 for proteins; the rest for RNAs).
• Mycoplasma urealyticum has 751,719 base pairs of DNA encoding 651 genes (613 for proteins; 39 for RNAs).
• Mycoplasma pneumoniae has 816,394 base pairs of DNA encoding 679 genes.

How many genes does it take to make an organism?

The scientists at The Institute for Genomic Research (now known as the J. Craig Venter Institute — JCVI) who determined the Mycoplasma genitalium sequence followed this work by systematically destroying its genes (by mutating them with insertions) to see which ones are essential to life and which are dispensable. Of the 485 protein-encoding genes, they have concluded that only 381 of them are essential to life.
Workers at the JCVI have also succeeded in synthesizing the complete genome of one species of mycoplasma, inserted this into a second species, which converted the second species into the first. Read more about this remarkable achievement.
Actinobacteria

Most of these Gram-positive organisms grow as thin filaments — like a mold — rather than as single cells. In fact, they were long thought to be fungi and were called actinomycetes. But fungi are eukaryotes and the actinobacteria are not.
Actinobacteria dominate the microbial life in soil where they play a major role in the decay of dead organic matter. Many of them have turned out to be the source of valuable antibiotics, including streptomycin, erythromycin, and the tetracyclines.
Mycobacteria and Corynebacteria

These Gram-positive organisms are closely related to the actinobacteria and often classified with them. They include three important human pathogens:

• Mycobacterium tuberculosis is the agent of tuberculosis (TB). TB is estimated to have killed 2 million people in 2007. Under ideal conditions, a single bacterium can cause infection. AIDS patients are especially at risk.Its genome contains 4,411,532 bp of DNA encoding some 3,959 genes.
• Mycobacterium leprae causes leprosy. Its genome contains 3,268,203 bp of DNA encoding only 1,604 genes. Although a close relative of M. tuberculosis (they share 1,439 genes), much of its DNA encodes pseudogenes, genes that no longer make a functional product. M. leprae is an obligate intracellular parasite; it has never been cultured in vitro. This is probably because it has abandoned many of the genes needed for an independent existence choosing instead to depend on the genes of its host cell.
• Corynebacterium diphtheriae causes diphtheria. As in tetanus, it isn't the growth of the organism (in the throat) that is dangerous but the toxin it liberates. The toxin is the product of a latent bacteriophage in the bacterium. It catalyzes the inactivation of a factor necessary for amino acids to be added to the polypeptide chain being synthesized on the ribosome. Sensibly enough, the toxin has no such effect on the translation machinery of bacteria (or of chloroplasts and mitochondria).Treatment of the toxin with formaldehyde converts it into a harmless toxoid. Immunization with this toxoid — usually incorporated along with tetanus toxoid and pertussis antigens in a "triple vaccine" (DTP) — protects against the disease.

The Proteobacteria

This large group of bacteria form a clade sharing related rRNA sequences. They are all Gram-negative but come in every shape (rods, cocci, spirilla).
They are further subdivided into 5 clades: alpha-, beta-, gamma-, delta-, and epsilon proteobacteria.
Alpha (α) Proteobacteria.

Some examples:

• Rickettsias. These bacteria are too small to be clearly seen under the light microscope. Almost all are obligate intracellular parasites. This means that they can only grow and reproduce while within the living cells of their host — certain arthropods (ticks, mites, lice, fleas) and mammals.
  • Rickettsia prowazekii causes typhus fever when it is transmitted to humans by lice.
  • Rocky Mountain spotted fever is a rickettsial disease transmitted by ticks.
  The mitochondria of eukaryotes probably evolved from endosymbiotic bacteria. Because of the similarities of their genomes, rickettsias may be the closest relatives to the ancestors of mitochondria.
• Rhizobia. These bacteria live in a mutualistic relationship with the roots of legumes where they are able to "fix" nitrogen (N2) in the air into compounds that can be used by living things.
• Magnetospirillum magnetotacticum
• Agrobacterium tumefaciens

Beta (β) Proteobacteria

• Sulfur bacteria. Certain colorless bacteria share the ability of chlorophyll-containing organisms to manufacture carbohydrates from inorganic raw materials, but they do not use light energy for this. These so-called chemoautotrophic bacteria secure the necessary energy by oxidizing some reduced substance present in their environment. The free energy released by the oxidation is harnessed to the manufacture of food.
  For example, some chemoautotrophic sulfur bacteria oxidize H2S in their surroundings (e.g., the water of sulfur springs) to produce energy:
  
  2H2S + O2 → 2S + 2H2O; ΔG = -100 kcal
  They then use this energy to reduce carbon dioxide to carbohydrate (like the photosynthetic purple sulfur bacteria).
  
  2H2S + CO2 → (CH2O) + H2O + 2S
• Iron bacteria.These chemoautotrophs are responsible for the brownish scale that forms inside the tanks of flush toilets. They complete the oxidation of partially oxidized iron compounds and are able to couple the energy produced to the synthesis of carbohydrate.
• NitrosomonasThis chemoautotroph oxidizes NH3 (produced from proteins by decay bacteria) to nitrites (NO2−). This provides the energy to drive their anabolic reactions. The nitrites are then converted (by other nitrifying bacteria) into nitrates (NO3−), which supply the nitrogen needs of plants.
• Three important human pathogens among the β-proteobacteria.
  • Neisseria meningitidis.Causes meningococcal meningitis, an extremely serious infection of the meninges that occasionally occurs in very young children and in military camps. There is a vaccine that is effective against several strains but unfortunately not the most dangerous one.
  • Neisseria gonorrhoeae. Causes gonorrhea, one of the most common sexually-transmitted diseases (STDs): over 300,000 cases were reported in the U.S. in 2009. In males, the bacterium invades the urethra causing a discharge of pus and often establishes itself in the prostate gland and epididymis. In females, it spreads from the vagina to the cervix and fallopian tubes. If the infection is untreated (penicillin is usually effective although strains resistant to it are now being encountered), the resulting damage to the fallopian tubes may obstruct the passage of eggs and thus cause sterility.
  • Bordetella pertussis; the cause of "whooping cough".

Gamma (γ) Proteobacteria

The largest and most diverse subgroup of the proteobacteria.
Some examples
<UL>Escherichia coli. The most thoroughly-studied of all creatures (possibly excepting ourselves). Its entire genome has been determined down to the last nucleotide: 4,639,221 base pairs of DNA encoding 4,377 genes. Lives in the human colon, usually harmlessly. However, water or undercooked food contaminated with the O157:H7 strain has caused severe — occasionally fatal — infections.
Salmonella enterica. Two major human pathogens:

• Salmonella enterica var Typhi. Causes typhoid fever, a serious systemic infection occurring only in humans. This microbe is also known as Salmonella typhi.
• Salmonella enterica var Typhimurium. Confined to the intestine, it is a frequent cause of human gastrointestinal upsets but is also found in many other animals (that are often the source of the human infection). Also known as Salmonella typhimurium.

Vibrio cholerae. Causes cholera, one of the most devastating of the intestinal diseases. The bacteria liberate a toxin that causes massive diarrhea (10–15 liters per day) and loss of salts. Unless the water and salts are replaced quickly, the victim may die (of shock) in a few hours. Like other intestinal diseases, cholera is contracted by ingestion of food or, more often, water that is contaminated with the bacteria.
Pseudomonas aeruginosa. A common inhabitant of soil and water, it can cause serious illness in humans with

• defective immune systems
• serious burns
• cystic fibrosis

Frequently encountered in hospitals and resistant to most antibiotics and disinfectants.
Yersinia pestis. This bacillus causes bubonic plague. It is usually transmitted to humans by the bite of an infected flea. As it spreads into the lymph nodes, it causes them to become greatly swollen, hence the name "bubonic" (bubo — swelling of a lymph node) plague. Once in the lungs, however, the bacteria can spread through the air causing the rapidly lethal (2–3 days) "pneumonic" plague. Untreated, ~30% of the cases of bubonic plague are fatal, and the figure for the pneumonic form reaches 100%.
The recurrent epidemics of the "black death" in Europe from 1347–1352, which killed off at least one quarter of the population, are thought to have been caused by this organism. DNA sequencing of samples retrieved from the bodies of plague victims of that era confirm this diagnosis.Why are the Gram-negative bacteria encased in two membranes while the Gram-positives have only one? Evolutionary biologist James Lake has proposed that the Gram-negatives arose by one single-membrane bacterial ancestor engulfing another. His analysis of many genes in the various bacterial groups indicate that the most probable ancestors of this possible endosymbiosis were a clostridium and an actinobacterium. Clostridia are the only Gram-positive bacteria that have photosynthetic members and because the photosynthetic apparatus in all photosynthetic Gram-negative bacteria is in the inner membrane, perhaps the actinobacterium was the host and the clostridium the endosymbiont.

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Obesity or stem cell research could win Nobel

STOCKHOLM (AP) — Two scientists who unlocked some of the mysteries linked to obesity or a professor who figured out how to make stem cells without human embryos could be candidates for the medicine award when the first of the 2011 Nobel Prizes are announced Monday.
The prize committees don't give any clues — they even keep nominations secret for 50 years — but winners usually have won many other awards and distinctions before they are considered for a Nobel.
Canadian-born Douglas Coleman and American Jeffrey Friedman have won several prizes for their discovery of leptin, a hormone that regulates food intake and body weight, and could be in the running for the coveted prize worth 10 million kronor ($1.5 million).
Last year, Coleman, of the Jackson Laboratory in Bar Harbor, Maine, and Friedman, of Rockefeller University in New York, received the Lasker Award, often seen as a precursor to the Nobel, for having shown that obesity is frequently linked to metabolic disruptions, or the lack of leptin, rather than being a self-induced problem.
Japanese Shinya Yamanaka, another potential Nobel candidate, offered the world of regenerative medicine a breakthrough with experiments showing that stem cells can be made from ordinary skin cells. The discovery led to a leap in stem cell research, reducing the need for using human embryos.
Yamanaka won the Lasker Award in 2009 and this year shared Israel's Wolf Prize. One out of three Wolf award-winners in chemistry, physics and medicine have also won a Nobel Prize.
Yamanaka, of Kyoto University in Japan and the Gladstone Institute of Cardiovascular Disease in San Francisco, could share the prize with British cloning pioneer John Gurdon or Canadian stem cell researcher James Till. Till discovered blood stem sells, which have saved the life of many thousands of leukemia patients.
"Gurdon's cloning technique and Yamanaka's stem cells are highly interesting in the field of basic science," wrote science reporter Karin Bojs of Swedish daily Dagens Nyheter, who has stood out as a leading Nobel guesser over the years. "But so far, not a single sick person has been cured with these discoveries. It is therefore possible that Yamanaka and Gurdon get to share the prize with Canadian James Till."
Bojs said other possible candidates for the prize are the American-French trio Ronald Evans, Elwood Jensen and Pierre Chambon for their research on nuclear hormone receptors, and American David Julius for his discoveries of the molecular mechanisms by which the skin senses pain, heat and cold.
"It will be awarded to fundamental discoveries that leads to an understanding of the human body and, or treatment or prevention of illnesses," said Nobel Prize Committee Secretary Goran Hansson, declining to give away more details.
He said there are so many Nobel-worthy achievements in medicine that it can be hard to select a winner.
In an unusual leak last year, a Swedish newspaper revealed the jury's selection — British test tube baby pioneer Robert Edwards — before the announcement. The committee has since applied even stricter rules on keeping their discussions and documents surrounding potential candidates secret.
But that doesn't keep people from making predictions.
The scientific department of Thomson Reuters, which analyzes high-impact academic papers to make predictions, suggested U.S. scientists Brian Druker, Nicholas Lydon, and Charles Sawyers, could be awarded for work related to Gleevec and Sprycel, drugs that transformed chronic myelogenous leukemia from a fatal cancer into a manageable chronic condition.
Its predictions also include Robert Langer and Joseph Vacanti "for their pioneering research in tissue engineering and regenerative medicine," as well as Jacques Miller, Robert Coffman and Timothy Mosmann for their discovery of two types of blood cells and their role in regulating immune responses.
The Nobel Prizes date back to 1901 after a will left behind by Swedish dynamite inventor Alfred Nobel, and medicine winners are typically awarded for a specific breakthrough rather than a body of research.
The other award categories include physics, chemistry, literature and peace. The economics award isn't technically a Nobel and was established by Sweden's central bank in 1968.
The prizes are handed out every year on Dec. 10, on the anniversary of Nobel's death in 1896.

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The word micro-organism is a general term for a (very) small organism, so small that the use of a microscope is required to see details of its structure. The study of micro-organisms (also known as microbes) is called microbiology, and it is increasingly relevant in Biology.

A virus is a very small creature and can not be seen by the naked eye. They can only be seen with the aid of a microscope. Their size is so small that their size can only be measured in micro-meters. The organism which is so small and is measured in micros are known as micro organisms

Main groups of micro-organismsStudy calledSpecialist called viruses
(not really living organisms like the rest)virology(virologist)bacteriabacteriology(bacteriologist)fungimycology(mycologist)possibly less important
protozoaprotozoology(protozoologist)algaealgology (phycology)algologist (phycologist)

Each of these groups includes organisms which can be seen to be useful to man (especially in the context of biotechnology), and others which are harmful (mainly because of diseases - of animals and plants, or spoilage - of stored products, especially food). There are broad similarities in the way that these micro-organisms grow, but there are distinct differences in detail which must be appreciated.

From a classification point of view, these micro-organisms are now thought to merit separating from other more familiar living organisms (Plants and Animals), so they have been given Kingdoms of their own:

Group of micro-organismKingdomBacteria and Blue-green "algae"MoneraProtozoa and AlgaeProtoctists (Protists)FungiFungi
(as a separate Kingdom, not a subdivision of the plants)

Viruses are categorised according to a different system, because they are so unlike the others.

MICRO-ORGANISMS CAUSING DISEASE

If a micro-organism has an adverse effect on another organism, e.g. causing a disease in Man, perhaps by getting inside and damaging its cells, or affecting it with a chemical substance which it produces, it is said to be pathogenic (adjective) or a pathogen (noun). It may also be described as the causative organism of that disease.

Pathogens can be said to be parasitic because they live at the expense of the other organism - their "host".


All viruses are pathogenic because they enter cells and cause adverse effects. Some of the worst diseases of Man are viral, i.e. caused by a virus.

Some bacteria (ones which cause headlines!) are pathogenic, and a few cause quite serious diseases. Other bacteria seem to be useful to Man in their correct contexts, whilst other apparently fairly harmless bacteria may cause diseases in certain circumstances, e.g. old or young people. In addition, there may be different varieties or strains (especially of bacteria and viruses) which show different characteristics from the normal type or species.

Similarly, there are examples of protozoans (protoctists) and fungi which are pathogenic.


Why are micro-organisms such powerful pathogens?

Size and distribution: Being so small, many micro-organisms can fit into a small space, or spread out (thinly!) over a large area, although most are not able to move of their own accord.

Reproductive --- Because they can multiply rapidly, it only takes a few bacteria or viruses to cause an infection. Usually, micro-organisms reproduce asexually, so they can produce millions in a few hours.


With such large potential populations, new varieties can arise due to mutation, and characteristics like resistance to antibiotics can spread easily, even between unrelated species!


They cannot be seen directly, and whilst reproducing and preparing to spread they can cause great damage to cells and internal working parts of organisms.

Viruses undergo genetic change by several mechanisms. These include a process called genetic drift where individual bases in the DNA or RNA mutate to other bases. Most of these point mutations are "silent" – they do not change the protein that the gene encodes – but others can confer evolutionary advantages such as resistance to antiviral drugs. Antigenic shift occurs when there is a major change in the genome of the virus. This can be a result of recombination or reassortment. When this happens with influenza viruses, pandemics might result. RNA viruses often exist as quasispecies or swarms of viruses of the same species but with slightly different genome nucleoside sequences. Such quasispecies are a prime target for natural selection.Segmented genomes confer evolutionary advantages; different strains of a virus with a segmented genome can shuffle and combine genes and produce progeny viruses or (offspring) that have unique characteristics. This is called reassortment or viral sex.
Genetic recombination is the process by which a strand of DNA is broken and then joined to the end of a different DNA molecule. This can occur when viruses infect cells simultaneously and studies of viral evolution have shown that recombination has been rampant in the species studied.Recombination is common to both RNA and DNA viruseS.




Penetration follows attachment: Virions enter the host cell through receptor-mediated endocytosis or membrane fusion. This is often called viral entry. The infection of plant and, it is presumed, fungal cells is different from that of animal cells. Plants have a rigid cell wall made of cellulose, and fungi one of chitin, so most viruses can get inside these cells only after trauma to the cell wall.However, nearly all plant viruses (such as tobacco mosaic virus) can also move directly from cell to cell, in the form of single-stranded nucleoprotein complexes, through pores called plasmodesmata. This process requires movement proteins, which are virus-encoded proteins probably originally derived from plant proteins, which interact with the plasmodesmatal transport machinery Bacteria, like plants, have strong cell walls that a virus must breach to infect the cell. However, given that bacterial cell walls are much less thick than plant cell walls due to their much smaller size, some viruses have evolved mechanisms that inject their genome into the bacterial cell across the cell wall, while the viral capsid remains outside



A typical virus replication cycle



Role in human disease


Examples of common human diseases caused by viruses include the common cold, influenza, chickenpox and cold sores. Many serious diseases such as ebola, AIDS, avian influenza and SARS are caused by viruses. The relative ability of viruses to cause disease is described in terms of virulence. Other diseases are under investigation as to whether they too have a virus as the causative agent, such as the possible connection between human herpes virus six (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome. There is controversy over whether the borna virus, previously thought to cause neurological diseases in horses, could be responsible for psychiatric illnesses in humans.Viruses have different mechanisms by which they produce disease in an organism, which largely depends on the viral species. Mechanisms at the cellular level primarily include cell lysis, the breaking open and subsequent death of the cell. In multicellular organisms, if enough cells die, the whole organism will start to suffer the effects. Although viruses cause disruption of healthy homeostasis, resulting in disease, they may exist relatively harmlessly within an organism. An example would include the ability of the herpes simplex virus, which causes cold sores, to remain in a dormant state within the human body. This is called latency and is a characteristic of the herpes viruses including Epstein-Barr virus, which causes glandular fever, and varicella zoster virus, which causes chickenpox and shingles. Most people have been infected with at least one of these types of herpes virus. However, these latent viruses might sometimes be beneficial, as the presence of the virus can increase immunity against bacterial pathogens, such as Yersinia pestis.Some viruses can cause life-long or chronic infections, where the viruses continue to replicate in the body despite the host's defence mechanisms. This is common in hepatitis B virus and hepatitis C virus infections. People chronically infected are known as carriers, as they serve as reservoirs of infectious virus. In populations with a high proportion of carriers, the disease is said to be endemic