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Cell Biology/Organelles

../Parts of the cell/

Organelles: (1) nucleolus (2) nucleus (3) ribosome (4) vesicle (5) rough endoplasmic reticulum (ER) (6) Golgi apparatus (7) Cytoskeleton (8) smooth ER (9) mitochondrion (10) vacuole (11) cytoplasm (12) lysosome (13) centrioles (14) vacuole

Nucleus
The nucleus contains genetic material or DNA in the form of chromatin, or, during mitosis or late interphase, chromosomes. All transcription and replication of genetic material take place within the nucleus, as does RNA processing. The nucleolus also resides within the nucleus and is responsible for RNA transcription and folding. Translation of RNA transcripts takes place outside of the nucleus.

Mitochondria
A mitochondrian is the organelle responsible for a cell's metabolism. It synthesizes ATP through a protein called ATP synthase. Mitochondria have a double membrane. An outer membrane and a folded inner membrane. The internal membrane, called the cristae is invaginated (folded or creased), to maximize surface area enabling it to hold more ATP syntheses. It is called as "the powerhouse of the cell" which is present in the eukaryotic organisms. It has matrix inside the inner membrane. It is in a rod shape structure.

Ribosomes
Ribosomes are responsible for protein synthesis. They are comprised of interacting protein and nucleic acid chains. Broadly, ribosomes are comprised of a large and a small subunit. The small subunit functions to attach to the mRNA strand and hold it in place during translation, while the large subunit holds and manufactures the growing polypeptide chain. The large subunit is further subdivided into the A (aminoacyl), P (peptidyl), and E (exit) binding sites.

Aminoacyl Binding Site The aminoacyl binding site binds a charged tRNA whose anticodon matches the codon in the A site.

Peptidyl Binding Site The peptidyl binding site contains the molecular machinery that transfers the bound polypeptide from the tRNA to the polypeptide chain, and holds the growing chain in place.

Exit Site The exit site is the terminal binding site for tRNA, where discharged tRNA's are released from the translation complex.

Endoplasmic Reticulum
The Endoplasmic Reticulum (ER) acts as a transport from the nucleus and ribosomes to the Golgi apparatus. There are two types of endoplasmic reticulum:

Smooth ER
Smooth ER act as transport for various things, mainly the RNA from the nucleus to the ribosomes (RNA is a small piece of the DNA code specifically designed to tell the ribosomes what to make). Smooth ER appears smooth in texture, hence the name. Smooth ER plays an important role in lipid emulsification and digestion in the cell.

Rough ER
Rough ER are "rough" because of the ribosomes embedded in them. The rough ER takes the protein to the Golgi apparatus to be packaged into vacuoles

Golgi Complex(apparatus)
The Golgi Complex basically functions as a "packaging center" for the cell, attaching "address labels" (functional groups) to various cell products to direct them to their respective locations, and "packaging" the products into vacuoles to ensure delivery. Anatomically, the Golgi Complex consists of layers of lipid membrane stacked one on top of another, with a cis face and a trans face. As the molecular product being packaged moves through the complex, various enzymes act upon it to induce vacuole formation and functional group attachment.

Vacuole
Vacuoles are cellular storage places. Like the cell membrane, they are comprised of a lipid bilayer that functions as a selectively permeable barrier to regulate movement of materials into and out of the compartment. They can serve a variety of purposes, storing food, water, or waste products, or immune functions such as containing dangerous materials or maintaining turgor pressure (in plants). Vacuoles serve very different purposes in plant cells than they do in animal cells.

Plant Cells In plants, vacuoles comprise a significant portion of the cell's total volume and often contribute significantly to the function of a differentiated cell. For example, vacuoles in stomata cells contain large numbers of potassium ions, which can be pumped in or out to open or close the stomata.

Animal Cells In animal cells, vacuoles serve more subordinate roles, such as assisting in endo- and exocytosis or basic storage of food and waste.

Central Vacuole The central vacuole is found only in plant cells. It is filled with water and is pressurised, like a balloon. This forces all the other organelles within the cell out toward the cell wall. This pressure is called turgor pressure and is what gives plants their "crisp" and firm structure.

Peroxisomes
Peroxisomes perform a variety of metabolic processes and as a by-product, produce hydrogen peroxide. Peroxisomes use peroxase enzyme to break down this hydrogen peroxide into water and oxygen.

Lysosomes
Lysosomes are vacuoles containing digestive and destructive membranes. In white blood cells, these are used to kill the bacteria or virus, while in tadpole-tail cells they kill the cell by separating the tail from the main body.

They also do much of the cellular digestion involved in apoptosis, the process of programmed cell death.

Biologia celular/Organelos

title: Cell Biology/Organelles


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Cell Biology/Genetic material

Cell Biology | Parts of the cell

 * 1) ../Prokaryotes/
 * 2) ../Eukaryotes/
 * 3) ../Nucleus/
 * 4) ../Nuclear membrane/
 * 5) ../Nucleolus/
 * 6) ../Codons/
 * 7) ../RNA polymerase/
 * 8) ../Histones/

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: Cell Biology/Genetic material


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Cell Biology/Energy supply

../Parts of the cell/

Chloroplasts are the organelles used for photosynthesis (a process that incorporates light energy into storage as chemical energy) whereas mitochondria used in respiration (a process that releases stored chemical energy). It assumed that you already know the information about these organelles explained in the organelles section. If you have not read the entries on chloroplasts and mitochondria from there yet, please go back and read them now.

Chemicals to know

 * 1) /Important chemicals/

Photosynthesis

 * 1) /Light Dependent Reactions/
 * 2) /Calvin-Benson Cycle/

Cellular Respiration

 * 1) /Glycolysis/
 * 2) /Krebs cycle/
 * 3) /Electron transport/

title: Cell Biology/Energy supply


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Cell Biology/Introduction/What is a cell

Cells are structural units that make up plants and animals; also, there are many single celled organisms. What all living cells have in common is that they are small 'sacks' composed mostly of water. The 'sacks' are made from a phospholipid bilayer membrane. This membrane is semi-permeable (allowing some things to pass in or out of the cell while blocking others). There exist other methods of transport across this membrane that we will get into later.

So what is in a cell? Cells are 90% fluid (called cytoplasm) which consists of free amino acids, proteins, carbohydrates, fats, and numerous other molecules. The cell environment (i.e., the contents of the cytoplasm and the nucleus, as well as the way the DNA is packed) affect gene expression/regulation, and thus are VERY important aspects of inheritance. Below are approximations of other components (each component will be discussed in more detail later):

Elements

 * 59% Hydrogen (H)
 * 24% Oxygen (O)
 * 11% Carbon (C)
 * 4% Nitrogen (N)
 * 2% Others - Phosphorus (P), Sulphur (S), etc.

Molecules

 * 50% protein
 * 15% nucleic acid
 * 15% carbohydrates
 * 10% lipids
 * 10% Other

Components of cytoplasm
The following is optional reading, as all cell components will be discussed in subsequent chapters.

 * Cytosol - contains mainly water and numerous molecules floating in it- all except the organelles.
 * Organelles (which also have membranes) in 'higher' eukaryotic organisms:
 * Nucleus (in eukaryotes) - where genetic material (DNA) is located, RNA is transcribed.
 * Endoplasmic Reticulum (ER) - Important for protein synthesis. It is a transport network for molecules destined for specific modifications and locations. There are two types:
 * Rough ER - Has ribosomes, and tends to be more in 'sheets'.
 * Smooth ER - Does not have ribosomes and tends to be more of a tubular network.
 * Ribosomes - half are on the Endoplasmic Reticulum, the other half are 'free' in the cytosol, this is where the RNA goes for translation into proteins.
 * Golgi Apparatus - important for glycosylation, secretion. The Golgi Apparatus is the "UPS" of the cell. Here, proteins and other molecules are prepared for shipping outside of the cell.
 * Lysosomes - Digestive sacks found only in animal cells; the main point of digestion.
 * Peroxisomes - Use oxygen to carry out catabolic reactions, in both plant and animals. In this organelle, an enzyme called catalase is used to break down hydrogen peroxide into water and oxygen gas.
 * Microtubules - made from tubulin, and make up centrioles,cilia,etc.
 * Cytoskeleton - Microtubules, actin and intermediate filaments.
 * Mitochondria - convert foods into usable energy. (ATP production) A mitochondrion does this through aerobic respiration. They have 2 membranes, the inner membranes shapes differ between different types of cells, but they form projections called cristae. The mitochondrion is about the size of a bacteria, and it carries its own genetic material and ribosomes.
 * Vacuoles - More commonly associated with plants. Plants commonly have large vacuoles.
 * Organelles found in plant cells and not in animal cells:
 * Plastids - membrane bound organelles used in storage and food production. These are similar to entire prokaryotic cells - for example, like mitochondria they contain their own DNA and self-replicate. They include:
 * Chloroplasts - convert light/food into usable energy. (ATP production)
 * Leucoplasts - store starch, proteins and lipids.
 * Chromoplasts - contain pigments. (E.g. providing colors to flowers)
 * Cell Wall - found in prokaryotic and plant cells; provides structural support and protection.


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Cell Biology/Introduction/Cell size

Size of Cells
Although it is generally the case that biological cells are too small to be seen at all without a microscope, there are exceptions as well as considerable range in the sizes of various cell types. Eukaryotic cells are typically 10 times the size of prokaryotic cells (these cell types are discussed in the next Chapter). Plant cells are on average some of the largest cells, probably because in many plant cells the inside is mostly a water filled vacuole.

So, you ask, what are the relative sizes of biological molecules and cells? The following are all approximations:

0.1 nm (nanometer) diameter of a hydrogen atom 0.8 nm Amino Acid 2 nm Diameter of a DNA Alpha helix 4 nm Globular Protein 6 nm microfilaments 7 nm thickness cell membranes 20 nm Ribosome 25 nm Microtubule 30 nm Small virus (Picornaviruses) 30 nm Rhinoviruses 50 nm Nuclear pore 100 nm HIV 120 nm Large virus (Orthomyxoviruses, includes influenza virus) 150-250 nm Very large virus (Rhabdoviruses, Paramyxoviruses) 150-250 nm small bacteria such as Mycoplasma 200 nm Centriole 200 nm (200 to 500 nm) Lysosomes 200 nm (200 to 500 nm) Peroxisomes 800 nm giant virus Mimivirus 1 µm (micrometer) (1 - 10 µm) the general sizes for Prokaryotes 1 µm Diameter of human nerve cell process 2 µm E.coli - a bacterium 3 µm Mitochondrion 5 µm length of chloroplast 6 µm (3 - 10 micrometers) the Nucleus 9 µm Human red blood cell 10 µm (10 - 30 µm) Most Eukaryotic animal cells (10 - 100 µm) Most Eukaryotic plant cells 90 µm small Amoeba 120 µm Human Egg up to 160 µm Megakaryocyte up to 500 µm giant bacterium Thiomargarita up to 800 µm large Amoeba 1 mm (1 millimeter, 1/10th cm) 1 mm Diameter of the squid giant nerve cell up to 40mm Diameter of giant amoeba Gromia Sphaerica 120 mm Diameter of an ostrich egg (a dinosaur egg was much larger) 3 meters Length of a nerve cell of giraffe's neck

What limits cell sizes?
 * Prokaryotes — Limited by efficient metabolism
 * Animal cells (eukaryotic) — Limited by surface area to volume ratio
 * Plant cells (eukaryotic) — Have large sizes due to large central vacuole, which is responsible for their growth

Related reading

 * Some early history related to the development of an understanding of the existence and importance of cells. The importance of microscopy.

title: Cell Biology/Introduction/Cell size


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Cell Biology/Introduction/The elements of life

The various elements that make up the cell are:

 * 59% Hydrogen (H)
 * 24% Oxygen (O)
 * 11% Carbon (C)
 * 4% Nitrogen (N)
 * 2% Others - Phosphorus (P), Sulfur (S), etc.

The difference between these elements is their respective atomic weights, electrons, and in general their chemical properties. A given element can only have so many other atoms attached. For instance carbon (C) has 4 electrons in its outer shell and thus can only bind to 4 atoms; Hydrogen only has 1 electron and thus can only bind to one other atom. An example would be Methane which is CH4. Oxygen only has 2 free electrons, and will sometimes form a double bond with a single atom, which is an 'ester' in organic chemistry (and is typically scented).

As for the organic molecules that make up a typical cell:

 * 50% protein
 * 15% nucleic acid
 * 15% carbohydrates
 * 10% lipids
 * 10% Other

Here is a list of Elements, symbols, weights and biological roles.


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Cell Biology/Introduction/What is living

The question, "What is life?" has been one of many long discussions and the answer may depend upon your initial definitions.

Life is cells. Cell theory consists of three basic points.
 * 1) All living things are made of cells.
 * 2) The cell is the smallest living thing that can perform all the functions of life.
 * 3) All cells must come from preexisting cells.

Some definitions of life are:
 * 1) The quality that distinguishes a vital and functional being from a non-living or dead body or purely chemical matter.
 * 2) The state of a material complex or individual characterized by the capacity to perform certain functional activities including metabolism, growth, and reproduction.
 * 3) The sequence of physical and mental experiences that make up the existence of an individual.

Seven Criteria
In biology, whether life is present is determined based on the following seven criteria:

 * 1) It should maintain some balanced conditions in its inner structure. This is called Homeostasis
 * 2) Its structure is highly organized.
 * 3) It should be able to break down or build up nutrients to release or store energy based on need. This is called Metabolism
 * 4) It should grow, which means its structure changes as time goes by in an advantageous manner.
 * 5) It should show adaptation to the environment.
 * 6) It should be able to respond to environmental stimuli on demand (as opposed to adaptation, which occurs over time).
 * 7) It should be able to reproduce itself.

Another way of remembering the seven life processes for children is:-

Movement Respiration Sensitivity Growth Reproduction Excretion Nutrition

Note the beginning letter of all the seven life processes, it spells out MRS GREN.

Virus Controversy
This definition of life has got some problems to it though: As an example, let's take viruses. Just by your intuition, what would you say: Are viruses alive or dead? Most people's intuitive answer is: Viruses are alive. When we suffer from any viral infection, we have the feeling that these viruses that cause our infection are alive. According to the seven principles as shown above, viruses are dead, as dead as a piece of plastic: They can't reproduce themselves. To understand that, we want to make a quick excursion to the replication mechanism of viruses: Viruses are really strange in their reproduction technique. Humans and other animals reproduce by the means of sexual intercourse, bacteria do something called binary fission: They divide. One cell divides itself into two, the two daughter cells divide again an so on. The point here is that both bacteria and animals or humans reproduce actively without any help from outside. Keep this point in mind as we move on to the viruses. Viruses need other cells to reproduce. They "drill" their way into another cell, called the host cell. Here, they release the genetic material they carry and, by a complex mechanism that shouldn't be explained further at this point, force their host cell to produce exact copies of the virus. After some time, the host cell is full of viruses and bursts, releasing the new viruses into the environment. Thus viruses need help to reproduce. They can't reproduce at all without a host cell and therefore do not fulfill the requirement "It should be able to reproduce itself". Looking at the other parts of the definition we find that viruses maintain some degree of homeostasis (1), being able to keep its protenatious and nucleic machinery separated from the outside world. Viruses also show adaptation(5), with their ability to mutate in order to affect new organisms. In addition to the reproduction problem, they also fail to meet the other requirements, showing no cellular organization (2) (or indeed cells at all), metabolism (3), or growth (4).

This example is just to illustrate the problems that arise using this definition. Life is not something one can define as any other technical term in science. Life arose from dead matter around 4 billion years ago. When life can arise from dead matter, there can't be a precise border line between these two.

The cell is alive, what about parts of it?
Organelles are parts of eukaryotic cells (ones having a nucleus). They help the cell carry out its task. But, are they alive? Do they meet 7 criteria?

When a cell divides into two, organelles also 'reproduce'. They also age from young to old and then die. Some of them carry out the task of taking food, converting it to nutrients and energy. They can also react to stimuli, and surely they can evolve. Of course one can argue that all the above are coordinated by the nucleus. But it seems there are some signs of life there.

Yes, there are! Scientists have proven that some bacteria, in its evolutionary way, had found a home in other cells. They felt comfortable when living there, and gradually, they have become a part of that cell. Chloroplasts, for example, used to be bacteria. At some point in their evolutionary history these cyanobacteria formed a mutual symbiosis with the proto-eukaryote ancestors of algae. Since that time, chloroplasts have been helping plant cells photosynthesize.

Another example is mitochondria, organelles that produce energy for eukaryotes. Very likely a parasitic organism originally, the ancestor of the mitochondria we see today colonized the larger proto-eukarotes. It is unknown if the mitochondrial ancestor originally had a metabolic role in its life cycle or if it adapted to the changing conditions after it was engulfed.


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Cell Biology/Introduction/Cell biology's interest

What makes Cell Biology particularly interesting is that there is so much that is not fully understood. A cell is a complex system with thousands of molecular components working together in a coordinated way to produce the phenomenon we call "life". During the 20th century these molecular components were identified (for example, see Human Genome Project), but research continues on the details of cellular processes like the control of cell division and cell differentiation. Disruption of the normal control of cell division can cause abnormal cell behavior such as rapid tumor cell growth.

Cells have complex interactions with the surrounding environment. Whether it is the external world of a single celled organism or the other cells of a multicellular organism, a complex web of interactions is present. Study of the mechanisms by which cells respond appropriately to their environments is a major part of cell biology research and often such studies involve what is called signal transduction. For example, a hormone such as insulin interacting with the surface of a cell can result in the altered behavior of hundreds of molecular components inside the cells. This sort of complex and finely tuned cell response to an external signal is required for normal metabolism and to prevent metabolic disorders like Type II diabetes.

Most of the cells of a multi-cellular organism have the same genetic material in every cell; yet, there may be hundreds of different types of cells that make up the organism's body each with its own distinctive shape, size, and function. In any case, all of these cells were developed from one special cell, a zygote. The study of how the many cell types develop during embryonic development (Developmental Biology) is a branch of Biology that is heavily dependent on the use of microscopy. Much of the control of cell differentiation is at the level of the control of gene transcription, the control of which mRNAs are made. Muscle cells make muscle proteins and nerve cells make brain proteins. Geneticists, molecular biologists and cell biologists are working to discover the details of how cells specialize to accomplish hundreds of functions from muscle contraction to memory storage.

Summary

 * Complexity in:
 * inter-relations between cells
 * signal transduction pathways inside cells
 * control of cell death and cell reproduction
 * control of cell differentiation
 * control of cell metabolism.


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Cell Biology/Cell types/Prokaryotes

Most of these prokaryotic cells are small, ranging from 1 to 10 microns with a diameter no greater than 1 micron. The major differences between Prokaryotic and Eukaryotic cells are that prokaryotes do not have a nucleus as a distinct organelle and rarely have any membrane bound organelles [mitochondria, chloroplasts, endoplasmic reticulum, golgi apparatus, a cytoskeleton of microtubules and microfilaments] (the only exception may be a bacterium discovered to have vacuoles). Both types contain DNA as genetic material, have a surrounding cell membrane, have ribosomes[70 s], accomplish similar functions, and are very diverse. For instance, there are over 200 types of cells in the human body, that vary greatly in size, shape, and function.

Prokaryotes are cells without a distinct nucleus.They have genetic material but that material is not enclosed within a membrane. Prokaryotes include bacteria and cyanophytes. The genetic material is a single circular DNA strand and is located within the cytoplasm. Recombination happens through transfers of plasmids (short circles of DNA that pass from one bacterium to another). Prokaryoytes do not engulf solids, nor do they have centrioles or asters. Prokaryotes have a cell wall made up of peptidoglycan. In majority of prokaryotes, the genome consists of a circular chromosome whose structure includes fewer proteins that found in the linear chromosomes of eukaryotes. Their chromosome is located in the nucleoid, a region of cytoplasm that appears lighter than surrounding cytoplasm in electron micrographs. Also, a single chromosome have much smaller rings of separately replication DNA called plasmids.

Cell Surface
Prokaryotic cell walls maintain cell shape, provide physical protection, and prevents the cell from bursting in a hypotonic environment. In hypertonic environment, most prokaryotes lose water and shrink away from their wall (plasmolyze). The cell walls of prokaryotes differ in molecular composition and construction from those of eukaryotes. The bacterial cell walls contain peptidoglycan, a network of modified-sugar polymers cross linked by short polypeptides. This molecular fabric encloses the entire bacterium and anchors other molecules that extend from its surface. Archaeal cell walls contain a variety of polysaccharides and proteins but lack peptidoglycan.

Gram-positive bacteria have simpler walls with a relatively large amount of peptidoglycan. It has a thick cell wall that traps the crystal violet in the cytoplasm. The alcohol rinse does not remove the crystal violet which masks the added red safanin dye.

Gram-negative bacteria have less peptidoglycan and are structurally more complex, with an outer membrane that contains lipopolysaccharides. It has a thinner layer of peptidoglycan, and it is located in a layer between the plasma membrane and an outer membrane. The crystal violet is easily rinsed from the cytoplasm, and the cell appears pink or red.

The cell wall of many prokaryotes is covered by a capsule, a sticky layer of polysaccharide or protein. The capsule enables prokaryotes to adhere to their substrate or to other individuals in a colony. Some capsules protect against dehydration, and some shield pathogenic prokaryotes from attack by their host's immune system. Some prokaryotes stick to their substrate or to one another by means of hair like protein appendages called fimbriae. They are also known as attachment pili. Fimbriae are usually shorter extension of the plasma membrane.

In uniform environment, flagellated prokaryotes move randomly, but in heterogeneous environment, many prokaryotes exhibit taxis, movement toward or away from a stimulus. For example, prokaryotes that exhibit chemotaxis change their movement pattern in response to chemicals. They move toward nutrients or oxygen (positive chemotaxis) or away from a toxic substance (negative chemotaxis).

Reproduction and Adaptation
Prokaryotes reproduce quickly in a favorable environment. By binary fission, a single prokaryotic cell divid into 2 cells, which then divide into 4, 8, 16, and on. Under optimal conditions, many prokaryotes can divide every 1-3 hours. However the cells eventually exhaust their nutrient supply, poison themselves with metabolic wastes, face competition from other microorganisms, or are consumed by other organisms. The prokaryotes are small, they reproduces by binary fission, and they have short generation times. The ability of some prokaryotes to withstand harsh conditions also contributes to their success. Certain bacteria develop resistant cell called endospores when an essential nutrient is lacking. The original cell produces a copy of its chromosome and surrounds it with a tough wall, forming the endospore. Water is removed from the endospore, and its metabolism halt. The rest of the original cell then disintegrates, leaving the endospore behind. Most endospore are so durable that they can survive in boiling water. In less hostile environments, endospore can remain dormant but viable for centuries, able to rehydrate and resume metabolism when their environment improves.

Due to their short generation times, prokaryotic populations can evolve substantially in short periods of time. The ability of prokaryotes to adapt rapidly to new conditions highlights the fact that although the structure of their cells is simpler than that of eukaryotic cells, prokaryotes are not "primitive" or "inferior" in an evolutionary sense. They are highly evolved, and their population have responded successfully to many different types of environmental challenges.

Rapid reproduction and mutation In sexually reproducing species, the generation of a novel allele by a new mutation is rare at any particular gene. Instead, most of the genetic variation in sexual populations results from the way existing alleles are arranged in new combinations during meiosis and fertilization. Prokaryotes do not reproduce sexually, so at first glance their extensive genetic variation may seem puzzling.

After repeated rounds of division, most of the offspring cells are genetically identical to the original parent cell; however owing to insertions, deletions, and base-pair substitutions in their DNA, some of the offspring cells may differ genetically. The new mutations, though individually rare, can greatly increase genetic diversity in specie that has short generation times and large population sizes. This diversity, in turn, can lead to rapid evolution: individuals that are genetically better equipped for their local environment tend to survive and reproduce more prolifically than less fit individuals.

Transformation and Transduction
In transformation, the genotype and possible phenotype of a prokaryotic cell are altered by the uptake of foreign DNA from its surroundings. For example, bacteria from a harmless strain of Streptococcus pneumonia can be transformed to pneumonia-causing cells if they are placed into a medium containing dead, broken-open cells of the pathogenic strain. This transformation occurs when a live nonpathogenic cell takes up a piece of DNA carry the allele for pathogenicity. The foreign allele is then incorporated into the cell's chromosome, replacing the existing nonpathogenic allele- an exchange of homologous DNA segments. The cell is now a recombinant: Its chromosome contains DNA derived from two different cells.

In transduction, bacteriophage carries bacterial genes from one hose cell to another; transduction is a type of horizontal gene transfer. For most phages, transduction results from accidents that occur during the phage reproductive cycle. A virus that carries bacterial DNA may not be able to reproduce because it lacks its own genetic material. However, the virus may be able to attach to another bacterium (a recipient) and inject the piece of bacterial DNA acquired from the first cell (the donor). Some of this DNA may subsequently replace the homologous region of the recipient cell's chromosome by DNA recombination. In such a case, the recipient cell's chromosome becomes a combination of NA derived from two cells; genetic recombination has occurred.

 Conjugation and Plasmids In a process called conjugation, genetic material is transferred between two bacterial cells ( of same or different species) that are temporarily joined. The DNA transfer is one way: One cell donates the DNA, and the other receives it. The donor uses sex pili to attach to the recipient. After contacting a recipient cell, each sex pilus retracts, pulling the two cells together, much like a grappling hook. A temporary "mating bridge" then forms between the two cells, providing an avenue for DNA transfer. In most cases, the ability to form sex pili and donate DNA during conjugation results from the presence of a particular piece of DNA called the F factor. The F factor consists about 25 genes, most required for the production of sex pili. The F factor can exist either as a plasmid or as a segment of DNA within the bacterial chromosome.

The F factor in its plasmid form is called F plasmid. Cells containing the F plasmid, designated F+ cells, function as DNA donors during conjugation. Cells lacking the F factor, designated F-, function as DNA recipients during conjugation. The F+ condition is transferable in the sense that an F+ cell converts and F- cell to F+ is a copy of the entire F+ plasmid is transferred.

Chromosomal genes can be transferred during conjugation when the donor cell's F factor is integrated into the chromosome. A cell with the F factor built into its chromosome is called an Hfr cell. Like an F+ cell, an Hfr cell functions as a donor during conjugation with an F- cell. When chromosomal DNA from an Hfr cell enters and F- cell, homologous regions of the HFr and F- chromosomes may align, allowing segments of their DNA to be exchanged. This results in the production of a recombinant bacterium that has genes derived from two different cells- a new genetic cariant on which evolution can act. Though these processes of horizontal gene transfer have so far been studied almost exclusively in bacteria, it is assumed that they are similarly important in archaea.

Diverse nutritional and metabolic adaptations
The mechanisms discussed in the previous section- rapid reproduction, mutation, and genetic recombination- underlie that extensive genetic variation found in prokaryotic populations. This variation is reflected in the nutritional adaptations found in prokaryotes. Like all organisms, prokaryotes can be categorized by their nutrition; how they obtain every and the carbon used in building the organic molecules that make up cells. Nutritional diversity is greater among prokaryotes than among eukaryotes: Every type of nutrition observed in eukaryotes is represented among the prokaryotes, along with some nutritional modes unique to prokaryotes. Phototrophs are the organisms that obtain energy from light. Chemotrophs are the organisms that obtain energy from chemicals. Organisms that need only an inorganic compound are called autotrophs. Heterotrophs require at least one organic nutrient to make other organic compounds. Combining these possibilities for energy sources and carbon sources results in four major modes of nutrition.

 Photoautotrophs: photosynthetic organisms that capture light energy and use it to drive the synthesis of organic compounds and other inorganic carbon compounds. Cyanobacteria and many other groups of prokaryotes are photoautotrophs, as are plants and algae.

Chemoautotrophs: also need only an inorganic compound; however, instead of using light as an energy source, they oxidize inorganic substance, such as hydrogen sulfide, ammonia, or ferrous ions. This mode of nutrition is unique to certain prokaryotes.

Photoheterotrophs: Harness energy from light but must obtain carbon in organic form. This mode is unique to certain marine and halophilic (salt-loving) prokaryotes.

Chemoheterotrphs: must consume organic molecules to obtain both energy and carbon. This nutritional mode is widespread among prokaryotes. Fungi, animals, most protists, and even some parasitic plants are also chemoheterotrophs.

The Role of Oxygen In Metabolism
Prokaryotic metabolism also varies with respect to oxygen. Obligate aerobes use oxygen for cellular respiration and cannot grow without it. Obligate anaerobes, however, are poisoned by oxygen. Some obligate anaerobes live exclusively by fermentation; other extract chemical energy by anaerobic respiration, in which substance other than oxygen such as nitrate ions or sulfate ions accept electrons at the "downhill" end of electron transport chains. Facultative anaerobes use oxygen if it is present but can also carry out anaerobic respiration or fermentation in an anaerobic environment.

 Nitrogen Metabolism Nitrogen is essential for the production of amino acids and nucleic acids in all organisms. Whereas eukaryotes can obtain nitrogen from only a limited group of nitrogen compounds, prokaryotes can metabolize nitrogen in a wide variety of forms. For example, some cyanobacteria and some methanogens covert atmospheric nitrogen to ammonia, a process called nitrogen fixation. The cells can then incorporate this "fixed" nitrogen into amino acids and other organic molecules. In terms of their nutrition, nitrogen-fixing cyanobacteria are some of the most self-sufficient organisms, since they need only light, carbon dioxide, nitrogen, water and some minerals to grow. Nitrogen fixation by prokaryotes has a large impact on other organisms. For example, nitrogen -fixing prokaryotes can increase the nitrogen but can use the nitrogen compounds that the prokaryotes produce from ammonia.

 Metabolic Cooperation Cooperation between prokaryotes allows them to use environmental resource they could not use as individual cells. In some cases, this cooperation takes place between specialized cells of a colony. For instance, the cyanobacterium Anabaena has genes than encode proteins for photosynthesis and for nitrogen fixation, but a single cell cannot carry out both processes at the same time. The reason is that photosynthesis produces oxygen which inactivates the enzymes involved in nitrogen fixation. Instead of living as isolated cells, anabaena forms filamentous colonies synthesis while a few specialized cells called heterocytes carry out only nitrogen fixation. Each heterocyte is surrounded by a thickened cell wall that restricts entry of oxygen produced by neighboring photosynthetic cells. Intercellular connections allow heterocytes to transport fixed nitrogen to neighboring cells and to receive carbohydrates.

Metabolic cooperation between different prokaryotic species often occurs in surface-coating colonies known as biofilms. Cells in a biofilm secrete signaling molecules that recruit nearby cells, causing the colonies to grow. The cells also produce proteins that stick the cells to the substrate and on to another. Channels in the biofilm allow nutrients to reach cells in the interior and wastes to be expelled. Biofilm damage industrial and medical equipment, contaminate products, and contribute to tooth decay and more serious health problems. In another example of cooperation between prokaryotes, sulfate-consuming bacteria coexist with methane-consuming archaea in ball- shaped aggregates on the ocean floor. The bacteria appear to use the archaea's waste products, such as organic compounds and hydrogen. In turn, the bacteria produce compounds that facilitate methane consumption by the archaea. This partnership has global ramifications.

Reference
Berg, Jeremy M., John L. Tymoczko, and Lubert Stryer. Biochemistry. 7th ed. New York: W.H. Freeman, 2012. Print.

Reece, Campbell, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minosky, and Robert B. Jackson. Biology. 8th ed. San Francisco: Cummings, 2010. Print.

title: Cell Biology/Cell types/Prokaryotes


text:
Cell Biology/Cell types/Eukaryotes

Eukaryotes house a distinct nucleus, a structure in which the genetic material (DNA) is contained, surrounded by a membrane much like the outer cell membrane. Eukaryotic cells are found in most algae, protozoa, all multicellular organisms (plants and animals) including humans. The genetic material in the nucleus forms multiple chromosomes that are linear and complexed with proteins that help the DNA 'pack' and are involved in regulation of gene expression.

The cells of higher plants differ from animal cells in that they have large vacuoles, a cell wall, chloroplasts, and a lack of lysosomes, centrioles, pseudopods, and flagella or cilia. Animal cells do not have the chloroplasts, and may or may not have cilia, pseudopods or flagella, depending on the type of cell.

Comparing Prokaryotic and Eukaryotic Cells
All cells have several basic features in common: they are all bounded by a selective barrier, plasma membrane. Cytosol is a jellylike substance that is semifluid. All cells contain chromosomes which carry genes in the form of DNA, and ribosomes that make proteins according to instructions from the gene. The major difference between prokaryotic and eukaryotic cells is the location of their DNA. In eukaryotic cell, DNA is found at the nucleus, which is bounded by a double membrane. (the word eukaryotic is from the Greek eu, true, and karyon, kernel, here referring to the nucleus).

Eukaryotic cells are much larger than prokaryotic cells; size is general aspect of cell structure that relates to function. The logistics of carrying out cellular metabolism sets limits on cell size. At the lower limit, the smallest cells, known are bacteria called mycoplasmas have diameters between 0.1 and 1.0mm. These are the smallest packages with enough DNA to program metabolism and enough enzymes and other cellular equipment to carry out the activities necessary for a cell to sustain itself and reproduce.

Metabolic requirements also impose theoretical upper limits on the size that is practical for a single cell. Plasma membrane functions as a selective barrier that allows sufficient passage of oxygen, nutrients, and wastes to service the entire cell. For each square micrometer of membrane, only a limited amount of a particular substance can cross per second, so the ratio of surface area to volume is critical. As a cell increases in size, its volume grows proportionately more than its surface area. Area is proportional to a linear dimension squared, whereas volume is proportional to the linear dimension cubed. Therefore a smaller object has a greater ration of surface area to volume.

The need for a surface area sufficiently large to accommodate the volume helps explain the microscopic size of most cells, and the narrow, elongated shapes of others, such as nerve cells. Larger organisms has more cells compare to smaller cells. High ratio of surface area to volume is especially important in cells that exchange a lot of material with their surroundings such as intestinal cells. Such cells may have many long, thin projections from their surface called microvilli, which increase surface area without an appreciable increase in volume.

Animal Cells
Flagellum: locomotion organelle present in some animal cells; composed of a cluster of microtubules within an extension of the plasma membrane.

Centrosome: region where the cell's microtubules are initiated contains a pair of centrioles which function is unknown.

Cytoskeleton: reinforces cell's shape, functions in cell movement components are made of protein. It includes microfilaments, intermediate filaments, and microtubules.

Microvilli: projections that increase the cell's surface area.

Peroxisome: organelle with carious specialized metabolic functions; produces hydrogen peroxide as a by-product, then converts it to water.

Mitochondrion: organelle where cellular respiration occurs and most ATP is generated.

Lysosome: digestive organelle where macromolecules are hydrolyzed.

Golgi apparatus: organelle active in synthesis, modification, sorting, and secretion of cell products.

Ribosomes: complexes (small brown dots) that make proteins; free in cytosol or bound to rough ER or nuclear envelope.

Plasma membrane: membrane enclosing the cell

Endoplasmic Reticulum (ER): network of membraneous sacs and tube; active in membrane synthesis and other synthetic and metabolic processes; has rough (ribosome-studded) and smooth regions. (Rough ER, and Smooth ER)

Nucleus: nucleus contains: Nuclear envelope: double membrane enclosing the nucleus; perforated by pores; continuous with ER                 Nucleolus: structure involved in production of ribosomes; a nucleus has one or more nucleoli Chromatin: material consisting of DNA and proteins; visible as individual chromosomes in a dividing cell

In animal cells, lysosomes, centrosomes with centrioles, and flagella are present but not in plant cells.

Plant Cell
Cell Wall: outer layer that maintains cell's shape and protects cell from mechanical damage; made of cellulose, other polysaccharide, and protein.

Plasmodesmata: channels through cell walls that connect the cytoplasms of adjacent cells.

Chloroplast: photosynthetic organelle; converts energy of sunlight to chemical energy stored in sugar molecules.

 Central vacuole: prominent organelle in older plant cells; functions include storage, breakdown of waste products, hydrolysis of macromolecules; enlargement of vacuole is a major mechanism of plant growth.

Nucleus: nucleus contains: Nuclear envelope: double membrane enclosing the nucleus; perforated by pores; continuous with ER                 Nucleolus: structure involved in production of ribosomes; a nucleus has one or more nucleoli Chromatin: material consisting of DNA and proteins; visible as individual chromosomes in a dividing cell

Golgi apparatus: organelle active in synthesis, modification, sorting, and secretion of cell products.

Endoplasmic Reticulum (ER): network of membraneous sacs and tube; active in membrane synthesis and other synthetic and metabolic processes; has rough (ribosome-studded) and smooth regions. (Rough ER, and Smooth ER)

Ribosomes: complexes (small brown dots) that make proteins; free in cytosol or bound to rough ER or nuclear envelope.

Cytoskeleton: reinforces cell's shape, functions in cell movement components are made of protein. It includes microfilaments, intermediate filaments, and microtubules.

In plant cell, chloroplasts, central vacuole, cell wall, and plasmodesmata are present but not in animal cells. Chromatin in the plant cell is a primary protein

Nucleus
The nucleus contains most of the genes in the eukaryotic cell; some genes are located in mitochondria and chloroplast. It is generally the most conspicuous organelle in a eukaryotic cell. The nuclear envelope encloses the nucleus, sparating its contents from the cytoplasm. The nuclear envelope is a double membrane, each a lipid bilayer with associated proteins. The envelope is perforated by pore structure that are about 100nm in diameter. At the lip of each pore, the inner and outer membranes of the nuclear envelope are continuous. Pore complex lines each pore and regulates the entry and exit of most proteins and RNAs, as well as large complexes of macromolecules. Except at the pores, the nuclear side of the envelope is lined by the nuclear lamina, a netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope. Also nuclear matrix, a framework of fibers extending throughout the nuclear interior, present.

Chromosomes are organized DNA units that carry the genetic information. Each chromosome is made up of material called chromatin, a complex of proteins and DNA. Stained chromatic usually appears as a diffuse mass, byt as a cell prepares to divide, the thin chromatin fibers coil up and condense thick enough to be distinguished as chromosomes. Each eukaryotic species has a characteristic number of chromosomes. For example human has 46 chromosomes.

Nucleolus is a prominent structure within the nondividing nucleus. Ribosomal RNA (rRNA) is synthesized from instructions in the DNA; in nucleolus, proteins imported from the cytoplasm are assembled with rRNA into large and small ribosomal subunits. Theses subunits then exit the nucleus through the nuclear pores to the cytoplasm, where a large and a small subunit can assemble into a ribosome. the number depends on the species and the stage in the cell's reproductive cycle.

The Nucleus directs protein synthesis by synthesizing messenger RNA (mRNA) according to instructions provided by the DNA. The mRNA is then transported to the cytoplasm via the nuclear pores. Once an mRNA molecule reaches the cytoplasm, ribosomes translate the mRNA's genetic message into the primary structure of a specific poly peptide.

Ribosomes
Ribosomes are complexes made of ribosomal RNA and protein; ribosomes are the cellular components that carry out proteins synthesis, also known as protein factories. Cells that have high rates of protein synthesis have particularly large number of ribosomes. Cells active in protein synthesis also have prominent nucleoli. Ribosomes build proteins in two cytoplasmic locales. Free ribosomes are suspended in the cytosol, while bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope. Bound and free ribosomes are structurally identical, and ribosomes can alternate between the two roles. Most of proteins are made on free ribosomes function within the cytosol. Bound ribosomes generally make proteins that are destined for insertion into membranes, for packaging within certain organelles such as lysosomes, or for export from the cell (secretion).

The Endomembrane System
Endomembrane system carries out a variety of tasks in the cell. These tasks include synthesis of proteins and their transport into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons. The membrane of this system are related either through direct physical continuity or by the transfer of membrane segments as tiny vesicles. The various membranes are not identical in structure and function; the thickness, molecular composition, and types of chemical reactions carried out in a given membrane are not fixed but modified several times during the membrane's life. The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, various kinds of vacuoles, and the plasma membrane.

Endoplasmic Reticulum (ER)
Endoplasmic reticulum (ER) is an extensive network of membrane that it accounts for more than half the total membrane in many eukaryotic cells. The word endoplasmic means "within the cytoplasm", and reticulum is Latine for "little net". The ER consists of a network of membranous tubules and sacs called cisternae. The ER membrane separates the internal compartment of the ER, ER lumen (cavity) or cisternal space, from the cytosol. Since ER membrane is continuous with the nuclear envelope, the space between the two membranes of the envelope is continuous with the lumen of the ER. Smooth ER lacks ribosomes on its outer surface, and Rough ER has ribosomes on the outer surface of the membrane. Ribosomes are also attached to the cytoplasmic side of the nuclear envelope's outer membrane.

Smooth ER- The smooth ER functions in diverse metabolic processes, which vary with cell type. These processes include synthesis of lipids, metabolism of carbohydrates, and detoxification of drugs and poisons. Enzymes of the smooth ER are important in the synthesis of lipids, including oils, phospholipids, and steroids. Sex hormones of vertebrates and the various steroid hormones are produced by the smooth ER in animal cells. Other enzymes of the smooth ER help detoxify drugs and poisons in liver cells. Detoxification involves adding hydroxyl groups to drug molecules, making them more soluble and easier to flush from the body. For example, sedative phenobarbital and other barbiturates are the drugs that metabolized in this manner by smooth ER in liver cells. Barbiturates, alcohol, and many other drugs induce the proliferation of smooth ER and its associated detoxification enzymes, therefore, increasing tolerance to the drugs; in other words, higher doses are required to achieve a particular effect. Also, because some of the detoxification enzymes have relatively broad action, the proliferation of smooth ER in response to one drug can increase tolerance to other drugs as well. The smooth ER also stores calcium ions; in muscle cells, a specialized smooth ER membrane pumps calcium ions from the cytosol into the ER lumen. When a muscle cell is stimulated by a nerve impulse, calcium ions rush back across the ER membrane into the cytosol and trigger contraction of the muscle cell.

Rough ER- Many times of cells secrete proteins produced by ribosomes attached to rough ER. As a polypeptide chain grows from a bound ribosomes, it is threaded into the ER lumen through a pore formed by a protein complex in the ER membrane. As the new protein enters the ER lumen, it folds into its native shape. Most secretory proteins are glycoproteins, which have carbohydrates covalently bonded to them. After secretory proteins are formed, the ER membrane keeps them separate from proteins that are produced by free ribosomes and will remain in the cytosol. Secretory proteins depart from the ER wrapped in the membranes of vesicles that bud like bubbles from a specialized region called transitional ER. Transport vesicles are the vesicles in transit from one part of the cell to another. Rough ER is also a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane. As polypeptide destined to be membrane proteins grow from the ribosomes, they are inserted into the ER membrane and are anchored there by their hydrophobic portions. The rough ER makes its own membrane phospholipids; enzymes build into the ER membrane assemble phospholipids from precursors in the cytosol. The ER membrane expands and is transferred in the form of transport vesicles to other components of the endomembrane system.

Golgi Apparatus
Golgi is a center of manufacturing, warehousing, sorting, and shipping. The products of the ER are modified and stored and then sent to other destinations. Golgi apparatus is extensive in cells specialized for secretion. The Golgi apparatus consists of flattened membranous sac, cisternae. The membrane of each cisterna in a stack separates ints internal space from the cytosol. Besicles concentrated in the vicinity of the Golgi apparatus are engaged in the transfer of material between parts of the Golgi and other structures. Golgi stack has a distinct structural polarity with the membrane of cisternae on opposite side of the stack different in thickness and molecular composition. The two poles of a Golgi stack are referred to as the cis face and the trans face; cis is the receiving and trans is shipping departments of the Golgi apparatus. The cis face is usually located near ER. Transport vesicles move material from the ER to the Golgi apparatus. A vesicle that buds from the ER can add its membrane and the contents of its lumen to the cis face by fusing with a Golgi membrane. The trans face give rise to vesicles, which pinch off and travel to other sites. The products of ER are usually modified during their transit from the cis region to the trans region of the Golgi. Various Golgi enzymes modify the carbohydrate portions of glycoproteins; carbohydrates are first added to proteins in the rough ER during the process of polypeptide synthesis. The carbohydrate on the resulting glycoprotein is then modified as it passes through the rest of the ER and the Golgi. The Golgi removes some sugar monomers and substitutes other, producing a large variety of carbohydrates. In addition, the Golgi apparatus manufactures certain macromolecules by itself. Many polysaccharides secreted by cells are Golgi products, including pectins and certain other non-cellulose polysaccharides made by plant cells and incorporated along with cellulose into their cell walls. Similar to secretory proteins, non-protein Golgi products will be secreted depart from the trans face of the Golgi inside transport vesicles that eventually fuse with the plasma membrane.

The Golgi manufactures and refines its products in stages, with different cisternae containing unique teams of enzymes. Recent research has give rise to a new model of the Golgi as a more dynamic structure; According to the cisternal maturation model, the cisternae of the Golgi actually progress forward from the cis to the tras face of the Golgi, carrying and modifying their cargo as they move. Before a Golgi stack dispatches its products by budding vesicles fromt he trans face, it sorts these products and targets them for various parts of the cell. Molecular identification tags, such as phosphate groups added to the Golgi products, aid in sorting. Transport vesicles budded fromt he Golgi may have external molecules on their membranes that recognize "docking site" on the surface of specific organelles or on the plasma membrane, therefore, targeting the vesicle appropriately.

Lysosomes
Lysosome is a membranous sac of hydrolytic enzymes that an animal cell uses to digest macromolecules. Lysosomal enzymes work best in the acidic environment found in lysosomes. If a lysosome breaks open or leaks its contents, the released enzymes are not very active because the cytosol has a neutral pH. However, excessive leakage from a large number of lysosomes can destroy a cell by autodigestion. Hydrolytic enzymes and lysosomal membrane are made by rough ER and then transferred to the Golgi apparatus for further processing. Proteins of the inner surface of the lysosomal membrane and the digestive enzymes are spared from destruction by having three dimensional shapes that protect vulnerable bonds from enzymatic attack.

Phagocytosis is a process that amoebas and many other protists eat by engulfing smaller organisms or other food particles. The food vacuole formed, and then fuses with a lysosome and digests the food. Digestion products pass into cytosol and become nutrients for the cell. In human body, white blood cell helps defend the body by engulfing and destroying bacteria and other invaders.

Lysosome use their hydrolytic enzymes to recycle the cell's own organic material; this is called autophagy. During autophagy, damaged organelle or small amount of cytosol become surrounded by a double membranes, and lysosome fuses with the outer membrane of their vesicle. The lysosomal enzymes dismantle the enclosed material, and the organic monomers are returned to the cytosol for reuse. The lysosomes become engorged with indigestible substrates, which begin to interfere with other cellular activities.

Vacuoles
Vacuoles are membrane-bounded vesicles whose functions vary in different kinds of cells. Food vacuoles are formed by phagocytosis. Many freshwater protists have contractile vacuoles that pump excess water out of the cell, thereby maintaining a suitable concentration of ions and molecules inside the cell. In plants and fungi, which lacks lysosomes, vacuoles carry out hydrolysis;

The central vacuole develops by the coalescence of smaller vacuoles, themselves derived from the endoplasmic reticulum and Golgi apparatus. The vacuolar membrane is selective in transportin solutes. As result, the solution inside the central vacuole is called cell sap, is different in composition from the cytosol. It can hold reserves of important organic compounds such as proteins stockpiled in the vacuoles of storage cells in seeds. Also it is the plant cell's main repository of inorganic ions, such as potassium and chloride. Many plant cells use their vacuoles contain pigments that color the cells. Vacuoles may also help protect the plant against predators by containing compounds that are poisonous or unpalatable to animals. The vacuole has a major role in the growth of plant cells, which enlarge as their vacuoles absorb water, enabling the cell to become larger with a minimal investment in new cytoplasm.

Mitochondria and Chloroplasts
Mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work. Mitochondria are the site of cellular respiration, the metabolic process that generates ATP by extracting energy from sugars, fats, and other fuels with the help of oxygen. Chloroplasts, are found in plants and algae, and they are the sites of photosynthesis. They convert solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugar from carbon dioxide and water. Both of them are not part of endomembrane system. Mitochondria have two membrane separating their innermost space from the cytosol, and chloroplasts have three. The membrane proteins of mitochondria and chloroplasts are made not by ribosomes bound to the ER, but by free ribosomes in the cytosol and by ribosomes contained within these organelles themselves. They also contain small amount of DNA that programs the synthesis of the proteins made on the organelle's ribosomes. Mitochondria and chloroplasts are semiautonomous organelles that grow and reproduce within the cell.

Mitochondria Mitochondria are found in all eukaryotic cells; Some cells have a single large mitochondrion, but more often a cell has hundreds or thousands of mitochondria. The number correlates with the cell's level of metabolic activity. The mitochondrion is enclosed by two membranes, each a phospholipid bilayer with a unique collection of embedded proteins. The outer membrane is smooth, but the inner membrane is convoluted, with infolding called cristae. The inner membrane divides the mitochondrion into two internal compartments : the first is the inter-membrane space, the narrow region between the inner and outer membranes and the second compartment, the mitochondrial matrix, is enclosed by the inner membrane. the matrix contains many different enzymes as well as the mitochondrial DNA and ribosomes. Enzymes in the matrix catalyze some steps of cellular respiration. Other proteins that function in respiration, including the enzyme that makes ATP are built into the inner membrane, As highly folded surface, the cristae give the inner mitochondrial membrane a large surface ares, thus enhancing the productivity of cellular respiration.

Chloroplasts The chloroplast is a specialized member of related plant organelles called plastids. Chloroplasts contain the green pigment chlorophyll, along with enzymes and other molecules that function in the photosynthetic production of sugar. Its shape is lens-shaped and found in leaves. The contents of a chloroplast are partitioned from the cytosol by an envelope consisting of two membranes separated by a very narrow intermembrane space. Inside the chloroplast is another membranous system in the form of flattened, inter-connected sacs called thylakoids. Thylakoids are stacked like poker ships, and each stack is called granum. The fluid outside the thylakoids is the stroma which contains the chloroplast DNA and ribosomes as well as many enzymes. The membranes of the chloroplast divide the chloroplast space into three compartments: the intermembrane space, the stroma, and the thylakoid space.

Cytoskeleton
Cytoskeleton is a network of fibers extending throughout the cytoplasm. It plays a major role in organizing the structure and activities of the cell. It is composed of three types of molecular structure: microtubules, microfilaments, and intermediate filaments. The main function of the cytoskeleton is to give mechanical support to the cell and maintain its shape. Cytoskeleton is stabilized by balance between opposing forces exerted by its elements. The cytoskeleton is more dynamic than an animal skeleton; it can be quickly dismantled in one part of the cell and reassembled in a new location, changing the shape of the cell. Also several types of cell motility involve the cytoskeleton. the cell motility encompasses both changes in cell location and more limited movements of parts of the cell. Cell motility require the interaction of the cytoskeleton with motor proteins. Cytoskeletal elements and motor proteins work together with plasma membrane molecules to allow whole cells to move along fibers outside the cell. The cytoskeleton is also involved in regulating biochemical activities in the cell in response to mechanical stimulation forces exerted by extracellular molecules via cell-surface proteins are apparently transmitted into the cell by cytoskeletal elements, and the forces may even reach the nucleus.

Microtubules- thickest

All eukaryotic cells have microtubules; the wall of the hollow tube is constructed from a globular protein called tubulin. Each tubulin protein is a dimer, a molecule made up of two subunits. A tubulin dimer consists of two slightly different polypeptides, alpha-tublin, and beta-tubulin. Microtubules grow in length by adding tubulin dimers. Due to the architecture of a microtubules, its two ends are slightly different; one end can accumulate or release tubulin dimers at a much higher rate than the other, therefore, growing and shrinking significantly during cellular activities. This is called the "plus end", not because it can only add tubulin proteins but because it's the end where both "on" and "off" rates are much higher. Microtubules shape and support the cell and also serve as tracks along which organelles equipped with other proteins can move.

In animal cells, microtubules grow out from a centrosomes, a region that is often located near the nucleus and considered a "microtubule-organizing center". Theses microtubules function as compression-resisting girders of the cytoskeleton. Within the centrosome are a pair of centrioles, each composed of nine sets of triplet microtubules arrange in a ring. Before division, the centrioles replicate; although centrosomes with centrioles may help organize microtubule assembly in animal cell,s they are not essential for this function in all eukaryotes.

Also specialized arrangement of microtubules is responsible for the beating of flagella and cilia. There are microtubule containing extensions that project from some cells. When cilia or flagella extend from cells that are held in place as part of a tissue layer, they can move fluid over the surface of the tissue. Flagella and cilia different in their beating patterns. A flagellum has an undulating motion that generates force in the same direction as the flagellum's axis. However cilia work more like oars, with alternating power and recovery strokes generating force in a direction perpendicular to the cilium's axis. A cillium may also act as a signal-receiving "antenna" for the cell. Cilia that have this function are nonmotile, and there is only one per cell. Membrane proteins on this kind of cilium transmit molecular signals from the cell's movement to its interior, triggering signaling pathways that may lead to changes in the cell's activities. Cillia-based signaling appears to be crucial to brain function and to embryonic development. Motile cilia and flagella share a common ultrastructure; each has a core of microtubules sheathed in an extension of the plasma membrane. Nine doublets of microtubules, the members of each parit sharing part of their walls, are arranged in a ring. This arrangement, referred to as the "9+2" pattern, is found in all eukaryotic flagella and motile cilia. Non-motile primary cilia have "9+0" pattern, lacking the central pari of microtubules. The microtubule assembly of a cilium or flagellum is anchored in the cell by a basal body, which is structurally very similar to a centriole.

In flagella and motile cilia, flexible cross-linking proteins, evenly spaced along the length of the cilium or flagellum, connect the outer doublets to each other and to the two central microtubules Each outer doublet also has paris of protruding proteins spaced along its length and reaching toward the neighboring doublet; These are large motor proteins called dyneins, composed of several polypeptides. Dyneins are responsible for the bending movements of the organelle. A dynein molecule performs a complex cycle of movements cause by changes in these shape of the proteins, with ATP providing the energy for these changes. The mechanics of dynein-based bending involve a process that resembles walking. A typical dynein protein has two "feet" that "walk" along the microtubule of the adjacent doublet, one foot maintaining contact while the other releases and reattaches one step further along the microtubules. Without any restraints ont he movement of the microtubules doublets, one doublet would continue to "walk" along and slide past the surface of the other, elongating the cilium or flagellum rather than bending it.

Microfillaments- thinnest

Microfilaments are solid rods about 7nm in diameter. They are also called as actin filaments because they are build from molecules of actin, a globular protein. A microfilament si a twisted double chain of actin subunits. Microfilaments can form structural networks, due to the presence of proteins that bind along the side of an actin filament and allow a new filament to extend as a branch. The structure role of microfilaments in the cytoskeleton is to bear tension. A cortical microfilaments, a three-dimensional network formed by microfilaments just inside the plasma membrane, helps support the cell's shape. This network give the outer cytoplasmic layer of a cell called the cortex.

In animal cells specialized for transporting materials across the plasma membrane, such as intestinal cells, bundles of microfilaments make up the core of microvilli. Microfillaments are well known for their role in cell motility, particularly as part of the contractile apparatus of muscle cells (myosin). Localized contraction brought about by actin and myosin also plays a role in amoeboid movement, which a cell such as an amoeba crawls along a surface by extending and flowing into cellular extension called pseudopodia. pseudopodia extend and contract through the reversible assembly of actin subunits nto microfilaments and of microfilaments into networks that convert cytoplasm fro a sol to a gel. The pseudopodium extends until the actin reassembles into a network.

In plant cells, both actin-myosin interactions and sol-gel transformations brought about by actin may be involved in cytoplasmic streaming, a circular flow of cytoplasm within cells.

intermediate filaments- middle range intermediate filaments are larger than the diameter of microfilaments but smaller than that of microtubules. Specialized for bearing tension (like microfilaments), intermediate filaments are a diverse class of cytoskeletal elements. Each type is constructed from a different molecular subunit such as keratins. Intermediate filaments are more permanent fixture of cells than are microfilaments and microtubules. Even after the death of the cell, intermediate filament networks often persist. Intermediate filaments are important in reinforcing the shape of a cell and fixing the position of certain organelles. For instance, the nucleus commonly sits within a cage made of intermediate filaments, fixed in location by braches of the filaments that extend into the cytoplasm. Other intermediate filaments make p the nuclear lamina that lines the interior of the nuclear envelope. In case where the shape of the entire cell is correlated with function, intermediate filaments support that shape.

Cell Wall
Cell wall is an extracellular structure of plant cell that distinguishes them from animal cells. The wall protects the plant cell, maintains its shape, and prevents excessive uptake of water. The strong walls of specialized cells hold the plant up against the force of gravity. Plant cell walls are much thicker than the plasma membrane, and the exact chemical composition of the wall varies from species to species and even from one cell type to another in the same plant, but basic design of the wall is consistent. Microfibrils made of the polysaccharide cellulose are synthesized by an enzyme called cellulose synthase and secreted to the extracellular space, where they become embedded in a matrix of other polysaccharides and proteins. This combination of materials, strong fibers in a "ground substance" (matrix), is the same basic architectural design found in steel-reinforced concrete and in fiberglass.

A young plant cell first secrets a thins and flexible wall called the primary cell wall; as the cell grows, the cellulose fibrils are oriented at right angles to the direction of cell expansion, possibly affecting the growth pattern. Between primary walls of adjacent cell is the middle lamella, which is a thin layer rich in sticky polysaccharides pectins. The middle lamella flues adjacent cells together. When the cell mature and stops growing, it strengthens its wall. Some plant cells do this simply by secreting hardening substances into the primary wall, but other cells add a secondary cell wall between the plasma membrane and the primary wall. Then secondary wall, often deposited in several laminated layer, has a strong and durable matrix that afford the cell protection and support.

title: Cell Biology/Cell types/Eukaryotes


text:
Cell Biology/Membranes/Phospholipids

Phospholipids | Cholesterol >>

Phospholipids are amphipathic molecules that are made up of a hydrophilic head and a hydrophobic  tail. The head group has a 'special' region that changes between various phospholipids. This head group will differ between cell membranes [types of cells] or different concentrations of specific 'head groups'. The fatty acid tails are also differ, but there is always one saturated and one unsaturated 'leg' of the tail.

Phospholipids are 2 fatty acids one saturated and one unsaturated (shown by the double bond) that are linked to a glycerol.

The Noncovalent Assemblies
For the phospholipid bilayer, even though it consists of hydrophilic heads on the outer membrane, the non-covalent hydrophobic tails of the inner membrane is the key to hold the entire membrane together because there are Van der Waals attractive forces within the cell membrane in which the hydrocarbon tails are closely packed together. With its non-covalent character inside the cell membrane, the hydrophobic molecules can easily pass through the cell membrane through passive diffusion. With this, the cell has control the molecules' movement through the transmembrane proteins complexes such as pores and gates. As for the hydrophilic molecules (such as ions, carbohydrates, proteins, amino acids, and nucleic acids), they require active diffusion in order to pass through the cell membrane because of their polarity and because they are hydrophilic (most non-covalent assemblies of the cell membrane are hydrophobic, such as hydrocarbon chains).

The non-covalent assemblies of the cell membrane can help give rise to bubbles such as liposome, or lipid vesicle, that can deliver drugs into a specific part of the body. The structure of liposome is very similar to the cell membrane's lipid bilayer, and the materials that compose the liposome is identical to cell membrane. Because liposome is a bubble, the structure is shaped like a ring, where the hydrophilic heads are the outer and inner ring while the hydrophobic tails are in between the hydrophilic heads' rings. Because of the ring structure, the liposomes are able to trap aqueous materials such as drugs into their rings. Once the materials are within the ring, the liposomes would deliver them to a specific location in the body, such as cancer cells.

title: Cell Biology/Membranes/Phospholipids


text:
Cell Biology/Membranes/Cholesterol

<< Phospholipids | Cholesterol | Semi-permeability and Osmosis >>

Cholesterol is a major component of cell membranes and serves many other functions as well. Cholesterol helps to 'pack' phospholipids in the membranes, thus giving more rigidity to the membranes. In colder conditions cholesterol also serves to keep the fluidity in the cell membrane, by keeping space in between the phospholipids. Also cholesterol serves diverse functions such as: it is converted to vitamin D (if irradiated with Ultra Violet light, modified to form steroid hormones, and is modified to bile acids to digest fats.

title: Cell Biology/Membranes/Cholesterol


text:
Cell Biology/Membranes/Semi-permeability and osmosis

<< Cholesterol | Semi-permeability and Osmosis | Proteins and channels >>

The membranes of cells are a fluid, they are semi-permeable, which means some things can pass through the membrane through osmosis or diffusion. The rate of diffusion will vary depending on the its: size, polarity, charge and concentration on the inside of the membrane versus the concentration on the outside of the membrane. When something is permeable it means that something can spread throughout, like (The perfume is permeating the room.). Here is a list of some molecules and how they relate to passing through the membrane without assistance, in other words, through diffusion:

Hydrophobic Molecules

 * O2 - Oxygen
 * N2 - Nitrogen
 * benzene

Small uncharged Polar Molecules

 * H2O - Water
 * urea
 * glycerol

Large Uncharged Polar Molecules

 * Glucose
 * Sucrose
 * nucletide

Ions

 * H+ - Hydrogen ion
 * Na+ - Sodium ion
 * K+ - Potassium ion
 * Ca2+ - Calcium ion
 * Cl- - Chloride ion

Various substances will pass through the membranes at varying rates through diffusion.


text:
User talk:Magnus Manske

Welcome to Wikibooks Magnus! You may be interested in checking out our Textbook planning page. --mav 21:11, 17 Aug 2003 (UTC)

Hi, I just wanted to say thanks for fixing the table on GCSE Science/Uses of static electricity :-) Theresa knott 21:46, 31 Aug 2003 (UTC)

Thank you very much Magnus for putting the books in the front page into tables. It looks great !! --Karl Wick

Hi,Magnus. I'm a biotech student ; just began to restructure the Proteins section. Still nothing written, but I think we need a good framework before,to organize content. What do you think about? Hope you like! Cyclop 13:37, 13 Apr 2004

Annotation
Magnus, what do we have to do to get the annotation stuff that you wrote implemented on the site ? We could really use it for the annotated books as well as the reg'lar books. Thanks man, --Karl Wick

Magnus, thanks for the tip about the content in your book that I can use in my organic chemistry book. I'll look over it and see what I can swipe. --Karl Wick

Copyright problem with Image:GENtle ligation.png
--Derbeth talk 09:54, 19 January 2006 (UTC)

 * Thanks a lot for your fast reaction. --Derbeth talk 09:43, 22 January 2006 (UTC)

Images with unknown copyright status
G'day Magnus, trawling through Category:Images with unknown copyright status, I see that a number of your earlier images have been listed. Could you please check them and specify their copyright status as appropriate? Here's a list of your image contributions, if that makes it easier. cheers, Webaware talk 07:00, 17 April 2007 (UTC)
 * G'day Magnus, thanks for clearing up those images. However, there are still some remaining images that have unknown copyright status:
 * Image:Bilayer.png
 * Image:Micelle.png
 * Image:Phospholipids.png
 * Image:Prokaryotes.png
 * Image:Small bilayer.png
 * It'd be great if you could nominate their sources and specify copyright status before one of the admins deletes them. Thanks, Webaware talk 13:25, 2 June 2007 (UTC)

 * Thanks mate, much appreciated. There's a push on to clean up unlicensed images, and I'd really like to keep as many as possible if they can be properly licensed somehow. cheers, Webaware talk 00:37, 20 June 2007 (UTC)

Isoschizomers
Hi Magnus, a useful tool for GENtle might be an option to hide isoschizomers for restriction enzymes. Does such an option exist which I have not yet found? The plasmid map can get pretty cluttered with the names of so many enzymes which cut at the same site. -Dave

title: User talk:Magnus Manske


text:
User talk:WouterVH~enwikibooks

Welcome to Wikibooks! --mav 21:11, 17 Aug 2003 (UTC)

Your account will be renamed
Hello,

The developer team at Wikimedia is making some changes to how accounts work, as part of our on-going efforts to provide new and better tools for our users like cross-wiki notifications. These changes will mean you have the same account name everywhere. This will let us give you new features that will help you edit and discuss better, and allow more flexible user permissions for tools. One of the side-effects of this is that user accounts will now have to be unique across all 900 Wikimedia wikis. See the announcement for more information.

Unfortunately, your account clashes with another account also called WouterVH. To make sure that both of you can use all Wikimedia projects in future, we have reserved the name WouterVH~enwikibooks that only you will have. If you like it, you don't have to do anything. If you do not like it, you can pick out a different name.

Your account will still work as before, and you will be credited for all your edits made so far, but you will have to use the new account name when you log in.

Sorry for the inconvenience.

Yours, Keegan Peterzell Community Liaison, Wikimedia Foundation 23:52, 17 March 2015 (UTC)

Renamed
 This account has been renamed as part of single-user login finalisation. If you own this account you can |log in using your previous username and password for more information. If you do not like this account's new name, you can choose your own using this form after logging in: . -- Keegan (WMF) (talk) 05:39, 19 April 2015 (UTC)

title: User talk:WouterVH~enwikibooks


text:
User talk:Tomos

Welcome to Wikibooks Tomos! You may be interested in our Textbook planning page. --mav 21:13, 17 Aug 2003 (UTC)

Tomos, apolgies for not seeing your WikiU comment sooner. A general answer that seems to apply to all your questions would be: Nobody knows yet since Wikiversity is just an idea some of us are kicking around. I've offloaded your question list to give it some thought, and will post some responses soon. Good work so far on Japaneese! Again, thanks for the thoughts, LouI 13:04, 7 Sep 2003 (UTC)

 * Thanks. And one more thanks for your comments! Tomos 16:19, 8 Sep 2003 (UTC)

title: User talk:Tomos


text:
Organic Chemistry/Overview of Functional Groups

Introduction
The number of known organic compounds is quite large. In fact, there are many times more organic compounds known than all the other (inorganic) compounds discovered so far, about 7 million organic compounds in total. Fortunately, organic chemicals consist of a relatively few similar parts, combined in different ways, that allow us to predict how a compound we have never seen before may react, by comparing how other molecules containing the same types of parts are known to react.

These parts of organic molecules are called functional groups. The identification of functional groups and the ability to predict reactivity based on functional group properties is one of the cornerstones of organic chemistry.

Functional groups are specific atoms, ions, or groups of atoms having consistent properties. A functional group makes up part of a larger molecule.

For example, -OH, the hydroxyl group that characterizes alcohols, is an oxygen with a hydrogen attached. It could be found on any number of different molecules.

Just as elements have distinctive properties, functional groups have characteristic chemistries. An -OH group on one molecule will tend to react similarly, although perhaps not identically, to an -OH on another molecule.

Organic reactions usually take place at the functional group, so learning about the reactivities of functional groups will prepare you to understand many other things about organic chemistry.

Memorizing Functional Groups
Don't assume that you can simply skim over the functional groups and move on. As you proceed through the text, the writing will be in terms of functional groups. It will be assumed that the student is familiar with most of the ones in the tables below. It's simply impossible to discuss chemistry without knowing the "lingo". It's like trying to learn French without first learning the meaning of some of the words.

One of the easiest ways to learn functional groups is by making flash cards. Get a pack of index cards and write the name of the functional group on one side, and draw its chemical representation on the other.

For now, a list of the most important ones you should know is provided here. Your initial set of cards should include, at the very least: Alkene, Alkyne, Alkyl halide (or Haloalkane), Alcohol, Aldehyde, Ketone, Carboxylic Acid, Acyl Chloride (or Acid Chloride), Ester, Ether, Amine, Sulfide, and Thiol. After you've learned all these, add a couple more cards and learn those. Then add a few more and learn those. Every functional group below is eventually discussed at one point or another in the book. But the above list will give you what you need to continue on.

And don't just look at the cards. Say and write the names and draw the structures. To test yourself, try going through your cards and looking at the names and then drawing their structure on a sheet of paper. Then try going through and looking at the structures and naming them. Writing is a good technique to help you memorize, because it is more active than simply reading. Once you have the minimal list above memorized backwards and forwards, you're ready to move on. But don't stop learning the groups. If you choose to move on without learning the "lingo", then you're not going to understand the language of the chapters to come. Again, using the French analogy, it's like trying to ignore learning the vocabulary and then picking up a novel in French and expecting to be able to read it.

Functional groups containing ...
In organic chemistry functional groups are submolecular structural motifs, characterized by specific elemental composition and connectivity, that confer reactivity upon the molecule that contains them.

Common functional groups include:

Note: The table above is adapted from the Functional Groups table on Wikipedia.

Combining the names of functional groups with the names of the parent alkanes generates a powerful systematic nomenclature for naming organic compounds.

The non-hydrogen atoms of functional groups are always associated with each by covalent bonds, as well as with the rest of the molecule. When the group of atoms is associated with the rest of the molecule primarily by ionic forces, the group is referred to more properly as a polyatomic ion or complex ion. And all of these are called radicals, by a meaning of the term radical that predates the free radical.

The first carbon after the carbon that attaches to the functional group is called the alpha carbon.

Alcohol containing two hydroxyl groups are called glycols. They have both common names and IUPAC names.

Mnemonics for Functional Groups
These are possible mnemonics for the common functional groups.

Vowels: Remember the vowels "A", "E", and "Y" for Alkane, Alkene, and Alkyne. Alkanes have only single covalent bonds. Alkenes have at least one double bond. Alkynes have at least one triple bond. The letters "I", "O", and "U" are not used. Furthermore, "O" and "U" would result in awkward pronunciations.

Alcohol: Look for the "C-O-H" in "Alcohol."

Ether: Ethers were anesthetics used in the 1800s. Dr. Kellogg also lived at the same time. Corn Flakes are made by Kellogg's. A rooster or cock (C-O-C) is the cornflake mascot. Or, think there is a C on "either" side of the O.

Amine: Remember the "N" stands for nitrogen.

Aldehyde: This sounds like "Adelaide," the Australian city. Australia is at the end of the Asian islands, and aldehydes are at the end of the hydrocarbon chain. The "Y" indicates a C=O double bond.

Ketone: Imagine the diagonal strokes of "K" forming the C=O double bond.

Carboxylic Acid: "Box" stands for boxed wine or C-O-H, alcohol. The "Y" indicates a C=O double bond.

Ester: This sounds like "Estelle" George Costanza's mother in the TV show Seinfeld. George's nickname was Koko or Coco. So think of O=C-O-C.

Amide: Amine with a "D". D for double.


text:
Abstract Algebra

This book is on abstract algebra (abstract algebraic systems), an advanced set of topics related to algebra, including groups, rings, ideals, fields, and more. Readers of this book are expected to have read and understood the information presented in the Linear Algebra book, or an equivalent alternative.

Table of Contents

 * 1) Introduction
 * 2) /Sets/
 * 3) /Equivalence relations and congruence classes/
 * 4) /Functions/
 * 5) /Binary Operations/
 * 6) /Linear Algebra/
 * 7) /Number Theory/
 * 8) Group Theory
 * 9) Groups
 * 10) Subgroups
 * 11) Cyclic groups
 * 12) Permutation groups
 * 13) Homomorphism
 * 14) Normal subgroups and Quotient groups
 * 15) Products and Free groups
 * 16) Group actions on sets
 * 17) /Composition series/
 * 18) The Sylow Theorems
 * 19) Rings
 * 20) /Rings/
 * 21) /Ring Homomorphisms/
 * 22) /Ideals/
 * 23) /Integral domains/
 * 24) /Fraction Fields/
 * 25) /Polynomial Rings/
 * 26) /Modules/
 * 27) /Projective line/
 * 28) Fields
 * 29) /Fields/
 * 30) /Factorization/
 * 31) /Splitting Fields and Algebraic Closures/
 * 32) /Separability, Normal Extensions/
 * 33) /Galois Theory/
 * 34) Vector Spaces
 * 35) /Vector Spaces/
 * 36) Algebras
 * 37) /Algebras/
 * 38) /Boolean algebra/
 * 39) /Clifford Algebras/
 * 40) /Shear and Slope/
 * 41) /Quaternions/
 * 42) /2x2 real matrices/
 * 43) /Hypercomplex numbers/
 * 44) Further abstract algebra
 * 45) /Category theory/
 * 46) /Lattice theory/
 * 47) /Matroids/
 * 48) /Authors/

Related books

 * See Subject:Algebra

Information for contributors

 * /Manual of Style/

Pages in progress
Abstract Algebra/The hierarchy of rings Abstract Algebra/Rings, ideals, ring homomorphisms

/Sources/

title: Abstract Algebra


text:
Japanese/Vocabulary/Everyday Phrases

see you

Greetings

 * 今晩は　(こんばんは) - Good evening (generally used after 6pm).
 * 今日は　(こんにちは) - Hello; good day; good afternoon.
 * おはよう - Casual "Good morning" (generally used until 10am).
 * おはようございます - Formal "Good morning."
 * お休み　(おやすみ) - Casual "Good night."
 * おやすみなさい - Formal "Good night."

Yes and No

 * はい - yes (formal)
 * ええ - yes (slightly less formal)
 * いいえ - no (formal)
 * うん - yeah/uh-huh (casual)
 * ううん - no/uh-uh (casual)
 * いや - no (casual, indicates displeasure)

Eating

 * いただきます - Polite phrase to say before eating.
 * ごちそうさまでした - Polite phrase to say after eating.

Praise

 * おめでとう - Congratulations
 * おめでとうございます - Stronger congratulations.
 * よく出来ました. - Good job. (You did well.)

Please and Thank You

 * ~ ください - ~ please. (Usually used with the -te form of the verb)
 * おねがいします - please (Slightly more polite)
 * どうぞ - please (Casual)
 * どうも - Thanks.
 * ありがとう - Thank you. (Casual)
 * どうもありがとう - Thank you very much. (Casual)
 * ありがとうございます - Thank you. (Polite)
 * どうもありがとうございます - Thank you very much. (Polite)
 * すみません - excuse me.
 * どうもすみません - Thanks a lot. (Usually when someone goes out of their way to help)
 * どういたしまして - You are welcome.
 * いいえ - Not at all/No problem.

Getting Attention

 * すみません - Excuse me.
 * あのうすみません - Ah, excuse me ...
 * すみませんが - Excuse me, but ...
 * おい - Hey (Somewhat rude)

Apology

 * ごめん - Sorry.
 * ごめんなさい - I am really sorry. (more formal)
 * ごめんね - Sorry (soft/fem.).
 * ごめんな - Sorry (masc.).
 * ごめんよ - Sorry (masc. or Kansai dialect).
 * すみません - I'm sorry.

Farewells

 * しつれいします. - goodbye for use with social superiors
 * さようなら - Goodbye. (Primarily before a long absence.)
 * じゃまた　- See you later.
 * じゃ - Bye! See you soon. (Mostly used by men )
 * じゃね - Bye! See you soon.(Mostly used by women)
 * また明日　(またあした) - See you tomorrow.
 * またね　- Later.
 * また会いましょう　(またあいましょう) See you again.
 * またどうぞ　- Please come again.
 * バイバイ - Borrowed from English, Bye Bye.
 * いってきます　- I'm leaving (said when leaving the house)
 * いってらっしゃい　- Have a safe trip (response to いってきます)
 * ただいま - I'm home (said when returning home)
 * おかえりなさい - Welcome back
 * おかえり - Less formal than the above

Finding the bathroom

 * トイレ (といれ) - Toilet
 * お手洗い (おてあらい) - Restroom (variants are 御手洗い and 手洗い)
 * 便所 (べんじょ) - Lavatory
 * 化粧室 (けしょうしつ) - Powder room

 * すみません. トイレはどこですか. - Excuse me. Where is the bathroom?
 * すみません. おはどちらですか. - Excuse me.  Which way is the restroom?

Hesitation noises
Hesitation noises, or vocal pauses, are the "uh" and "um" of a language, filler sounds we produce when we pause to think while speaking. Using the correct hesitation noises can make the difference between natural sounding Japanese, and awkward foreign sounding speech.

They are:
 * あのう - Usually when you are about to say something.
 * ええと - When you are just thinking.
 * まぁ　 - "Well..." used for considering, reconsidering, etc...
 * さぁ　 - Another thinking sound) Used for when you're not sure of the information.
 * 何だっけ (なんだっけ) - "What's it called..." used when trying to remember something specific.
 * そうですね - Acknowledges what was previously said. More of a staller than a hesitation noise.  Somewhat more formal. Also used to show you care what the speaker is saying.

title: Japanese/Vocabulary/Everyday Phrases