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By: Lauren and Christina

__Gene Regulation in Eukaryotes__

source: [|http://library.thinkquest.org/C004535/media/eukaryote_plant.gif]

Eukaryotic genes have introns and a large number of control elements. These control elements are non-coding DNA that help regulate transcription by binding proteins called transcription factors. A promotor region is a DNA sequence where RNA polymerase binds to start transcription and every eukaryotic gene contains it. The chromatic structure of the DNA can affect the ability of transcritional regulatory proteins. It also affects RNA polymerases to find access to specific genes and to activate transcription in them. The presence of the histones and the CpG methylation affects accessibility of the chromatin to RNA polymerase and transcription factors.

The transcriptional initiation is the most important mode for the control of eukaryotic gene expression. There are however other factors that supplement transcriptional regulation, like altering the rate at which RNA transcripts are processed while still within the nucleus. Also, altering the stability of mRNA molecules, and the efficiency at which the ribosomes translate the mRNA into polypeptide. The transcription start site is where a molecule of RNA 2 binds. The start site can be considered as the start site where transcription of teh gene into RNA begins. Enhancers are transcription factors that bind to the regions of DNA and are thousands of base pairs away from the gene they control. This binding then increases teh rate of transcription of the gene. Source: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Promoter.html

__Prokaryotes__

[|http://www.blobs.org/science/cells/prokaryote.gif]

Prokaryotes are a certain type of unicellular organism. They lack the organelles (to be explained later) that eukaryotic cells have, but they may contain the membrane systems inside a cell wall. Prokaryotic cells may also contain photosynthetic pigments, like the type that is found in cyanobacteria ("blue bacteria"). Certain prokaryotes may have flagella on the outside for locomotive purposes. Flagella are wonderful "motors" for swimming, but they only allow the prokaryote to move in two directions and at one speed. When going forward, is propelled in one direction at 30 mph. In reverse, prokaryotes have to do flips or tumbles. Prokaryotes cannot stop moving, either. Others have hair, like pili, for adhesion.

Prokaryotes can come in many different shapes: cocci (a round shape), baccilli (rod-shaped), or spirilla/spirochetes (helical cells). Prokaryotes have 0.001 times a much DNA as a eukaryote. While prokaryotes can "learn," they divide every twenty minutes, and thus have to restart their "education". Prokaryotes can have sex, when males possessing a sexual apparatus for transferring genetic information and receptive females are present. But, because both prokaryotes are going 30 mph, possibly in different directions, it's difficult to find "the one." Even worse, if you're a male, nature has given you a severe problem, different than the mental issues most male humans have. Everytime a male mates with a female prokaryote, //she// turns into a male, too! If that's not bad enough for you, at fairly high frequencies, spontaneous mutations can cause a male to turn into a female. Talk about losing your "man"-status.

Sources: [|http://www.biology.arizona.edu/Cell_BIO/tutorials/pev/page2.html]

__Viruses__

Source: [|http://www.ucmp.berkeley.edu/alllife/virus.gif]

Basically, viruses are simply genetic information surrounded by a protein coat. They can contain external structures and a membrane. Viruses are "obligate intracellular parasites"--in other words, they require host cells for reproduction. In the viral life cycle, first a virus infects a cell. That allows the viral genetic information to direct the synthesis of new virus particles by the cell it infected (talk about dominating)! And then, the virus ruptures the cell, so it can go and start over its life cycle in some other poor victim cell.

There are many different strains of viruses. Infectious viruses to humans include: polio, influenza ("the flu"), herpes, smallpox, chickenpox, and Human immodeficiency virus (HIV), which leads to AIDS. Some more viruses are the common cold (which is commonly caused by the Rhinovirus), shingles, rabies (a.k.a. hydrophobia), hanta fever, and Ebola. Some viruses even cause a few kinds of cancer! And that's only in humans--viruses can even infect other organisms, such as other eurkaryotes, as well! But viruses aren't always so bad--they can be utilized to transfer genetic material between different species of host, and are used extensively in genetic engineering. Viruses can cause transduction, a.k.a. "natural genetic engineering," in which it may incorporate some genetic material from its host as it's replicating, and transfer that newly-incorporated genetic information to a new host, maybe even to a host unrelated to the previous host! In some cases, transduction may serve as a means of evolutionary change, although it should be noted that it is not clear how important an evolutionary mechanism transduction actually is.

Sources: http://images.google.com/imgres?imgurl=http://www.ucmp.berkeley.edu/alllife/virus.gif&imgrefurl=http://www.ucmp.berkeley.edu/alllife/virus.html&h=555&w=402&sz=14&hl=en&start=1&tbnid=TGvlm0jZKP7I1M:&tbnh=133&tbnw=96&prev=/images%3Fq%3Dvirus%26gbv%3D2%26hl%3Den%26ie%3DUTF-8, [|http://www.biology.arizona.edu/Cell_BIO/tutorials/pev/page4.html], http://www.web-books.com/mobio/free/Ch1E3.htm, [|http://www.mcb.uct.ac.za/tutorial/viruscyc2.htm], [|http://www.health.state.ny.us/diseases/communicable/rabies/fact_sheet.htm]

__Prions__

Source: [|http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/prion.jpg]

Just about everyone has heard of "mad-cow disease," though hardly anyone actually knows what it is. Mad-cow disease, also known as Bovine Spongiform Encephalopathy (BSE), is one of many spongiform encephalopathies caused by "bad proteins," a.k.a. prions. Prions do not have a nucleid acid genome, meaning that the protein //alone// is the infectious agent. Prions are scientifically defined as "small proteinaceous infectious particles which resist inactivation by procedures that modify nucleic acids." This discovery that proteins alone can transmit infectious diseases has come as a suprise to the scientific and medical communities.

Diseases caused by prions tend to be called spongiform encephalopathies, due to the post mortem appearance of the brain. The brain has large vacoules (vacant holes) in the cortex and cerebellum. It is possible that most mammalian species develop these diseases. Some examples are scrapie (present in sheep and goats), TME (transmissible mink encephalopathy, obviously present in mink), CWD (chronic wasting disease, present in muledeer and elk), Exotic ungulate encephalopathy (EUE) (present in nyala & greater kudu), Feline spongiform encephalopathy (FSE) (present in cats), and BSE (bovine spongiform encephalopathy, present in cows). Some spongiform encephalopathies that humans are susceptible to are CJD (Creutzfeld-Jacob Disease), GSS (Gerstmann-Straussler-Scheinker syndrome), FFI (Fatal familial Insomnia), Kuru, and Alpers Syndrome.

Sources: [|http://www.tulane.edu/~dmsander/WWW/335/Prions.html], [|http://images.google.com/imgres?imgurl=http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/prion.jpg&imgrefurl=http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olprotaggreg.html&h=360&w=360&sz=43&hl=en&start=14&tbnid=2Pk5Vog5SAAglM:&tbnh=121&tbnw=121&prev=/images%3Fq%3Dprion%26gbv%3D2%26hl%3Den%26ie%3DUTF-8], [|http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/fs_prion.htm], [|http://www.cdc.gov/ncidod/dvrd/prions/]

__Mitochondria__

Source: http://micro.magnet.fsu.edu/cells/mitochondria/mitochondria.html

Mitochondria are a eukaryotic cell's "powerhouse." They are rod-shaped organelles that convert oxygen and nutrients into adenosine triphosphate (ATP). ATP is the chemical energy "currency" of the cell. It powers the the cell's metabolic activities. This process is known as aerobic respiration. It is reason animals breathe oxygen.

Mitochondria (//mitochondrion// for singular) are probably the reason higher animals exist. Without mitochondria, their cells would only be able to obtain energy from anaerobic respiration (which is respiration in the absence of oxygen). It is a process that is much less effecient than aerobic respiration. Mitochondria actually allow the cells they inhabit to produce 15 times more ATP than they could otherwise. That is very important because complex animals, such as humans and other mammals, need large amounts of energy in order to survive.

Source: http://micro.magnet.fsu.edu/cells/mitochondria/mitochondria.html

__Nucleus__

Source: http://www.microscopy.fsu.edu/cells/nucleus/images/nucleusfigure1.jpg

The nucleus is the "brain" of a eukaryotic organism. It is a highly specialized organelle that is present in eukaryotic organisms. It serves as the genetic information center for the cell. It also is the administrative center for the cell, and it coordinates the cell's activities, like growth, intermediary metabolism, protein synthesis, and reproduction (a.k.a. cell division). It regulates processes, such as what enters and exits the cell.

The nucleolus is a prominent sub-nuclear structure. It's not bound by a membrane and is within the nuclear matrix. Even though its existence has been known since the 1700's, the primary function was only discovered in the 1960's. It's now known that the purpose of nucleoli (which is plural for //nucleolus//) is to manufacture the subunits that combine and form the ribosomes, which produce proteins. Accordingly, a nucleolus' size varies depending on the cells ribosomal needs.

Source: http://images.google.com/imgres?imgurl=http://www.microscopy.fsu.edu/cells/nucleus/images/nucleusfigure1.jpg&imgrefurl=http://www.microscopy.fsu.edu/cells/nucleus/nucleus.html&h=266&w=359&sz=35&hl=en&start=6&sig2=hhjf35iIzVJd7w1u6A1M0Q&um=1&tbnid=PqWl9XHUB0jszM:&tbnh=90&tbnw=121&ei=30OmR8DNAY-keZb8tewC&prev=/images%3Fq%3Dnucleus%2B%26um%3D1%26hl%3Den%26sa%3DN%26ie%3DUTF-8

__Animal Heart Beats Back to Life__

Recently scientists coaxed recycled hearts that were taken from dead animals into beating. This happened in the laboratory after the scientists reseeded them with live cells. Although there have been advances in generating living heart tissue in the lab, this was the first time an entire heart has been brought back to life. The researchers have been seeking new treatments for heart disease and managed to grow a rat heart in the lab and then began the process of making it start to beat. Although this process seemed impossible, a procedure called decellularisation proved successful. In this process, first all of the cells from an organ (in this case, a heart) are stripped away by using powerful detergents, and then leaving only a bleached-white scaffolding composed of proteins secreted by the cells. Source: [|http://www.rat-patrol.org/RatHeartAn.gif] Although this is a big advancement in seeking new treatments for heart disease, researchers still have a very long way to go. The researchers' next step is to use a pig heart, strip away its cells and then repopulate it with the cells from a pig. Then they will see if this process will work in a larger heart instead of a small one like the rat heart. Some researchers that were not a part of this experiment note that this process was done in a small animal and we will have to wait and see if this same process can also be done in a larger host organism. This is still an important contribution, but with more work to be done. The researchers are also trying to reseed the cells in other organs including the lungs, liver, and kidneys. Sources: [|http://www.msnbc.msn.com/id/22635550/print/1/displaymode/1098/] [|http://www.chron.com/disp/story.mpl/health/5450985.html]

__DNA Mutations__ Source __:__ [|http://www.dkimages.com/discover/previews/834/60011169.JPG] Mutations occur in many different ways. The mutations can occur because of simple copying errors when DNA replicates itself. The mutation can also occur becuase of environmental changes like sunlight and radiation. Although our cells do have mechanisms which are built in to our DNA, as we age our DNA repair does not work as well. A result is that we then accumulate changes in our DNA. These mutations can occur in the cells of the body, or can occur in the DNA of cells that produce the eggs and sperm. The bases of DNA can be A, T, G, and C, and if any of these bases and if any of these instructions are altered, then the gene's meaning is altered.

There are multiple types of gene mutations. A point mutation is a simple change in one base of the gene sequences. This can also be equivalent to changing one letter in a sentence. There are also frameshift-mutations, which one or more bases are inserted or deleted. Unlike point mutations, frame-shift mutations is equivalent to adding or deleting a letter. Another type of mutation is deletion, whichare mutations that result in missing DNA. The deletions can be small, for example like deleting one word of an essay or longer deletions like multiple sentences in an essay. The last two types of muations are inversion and DNA expression mutation. Inversion is when an entire section of DNA is reversed, and DNA expression is when proteins are made in the worng time or wrong place (type of cell). Source: [|http://www.genetichealth.com/G101_Changes_in_DNA.shtml]

__Photosynthesis__ Source: [|http://www.factmonster.com/images/photosynthesis.gif] The process in which plants convert light energy to chemical energy and also store it is called photosynthesis. This process can also occur in come algae. The process of photosynthesis occurs in the chloroplasts, using chlorophyll. Chlorophyll is the green pigment involved in photosynthesis. Plants only need light energy, CO^2, and H^2O to make the sugar. The parts of the leaf that contain chloroplasts and in other words, in which photosynthesis occurs is in the mesophyll.

The parts of the chloroplast include stroma, intermembrane space, thylacoids stacked in grana, and the outer and inner membranes. The chloropyll may look green, however, it aborbs red and blue light. The green light, that is not absorbed is what we see with our eyes but the red and blue light are absorbed and used in photosynthesis. The two parts of photosynthesis are light and dark reactions. The light reaction happens in the thylakoid membrane and it also converts light energy to chemical energy. However, the dark reactions occur in teh stroma within the chloroplast, and also converts CO^2 to sugar. It doesn't directly need light for the reaction to occur but it needs the ATP and NADPH from the light reaction. Source: [|http://biology.clc.uc.edu/Courses/bio104/photosyn.htm]

__Chemical Bonding__

Source: http://publications.nigms.nih.gov/chemhealth/images/ch1_bonds.gif Chemical compounds are formed when two or more atoms join together. A compound that is stable occurs only when the total energy of the combination has lower energy than the separated atoms. When it is in a bound state, then it is implied that a net attractive force between is the atoms, or in other words, a chemical bond has occurred. The two most common cases are covalent bonds and ionic bonds. However, there are still other types of bonds, which include metallic and hydrogen bonds. Covalent bonds are bonds where one or more pairs of electrons are shared by two atoms.The type of covalent bonds that are not shared are called polar covalent bonds. The ionic bonds are the transfer of electrons. When the bond deals with metals, which possess strong bonds, but have the heat and electricity to have its electrons move freely in all directions, it is called a metallic bonds. Hydrogen bonds are the force of attraction between a hydrogen atom in one molecule and a small atom of high electronegativity in another molecule. Source: http://hyperphysics.phy-astr.gsu.edu/hbase/chemical/bond.html

__Cellular Respiration__ Source: http://bioweb.cs.earlham.edu/9-12/cellularrespiration/IMAGES/proton.JPG Cellular Respiration is the process of oxidizing food molecules, for example like glucose, to carbon dioxide and water. The energy that is then released is trapped and is in the form of ATP. This ATP is used for all energy-consuming activities of the cell. This process occurs in two phases: glycolysis and oxidation of pyruvate acid. Glycolysis is the breakdown of glucose to pyruvic acid. Then the complete oxidation of pyruvate acid to carbon dioxide and water. The process of glycolysis occurs in the cytosol and the remaining process occurs in the mitochondria. The mitochonria are membrane-enclosed organelles distributed through the cytosol of most eukaryotic cells, more was disccussed about the mitochondria earlier on this page. Also, the place where a complex mixture of soluble enzymes that catalyze the respiration of pyruvic acid and other small organic molecules being held is called the matrix. Then the Citric Acid Cycle results in a citric acid regenerates a molecule of oxaloacetic acid. The Electron Transport Chain is then also used in which it transfers the electrons from NADH to oxygen molecules then to form water molecules. Source: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellularRespiration.html

__Protists__ Source: http://www.dkimages.com/discover/previews/801/908566.JPG Protists are considered to be eukaryotes because they have a nucleus. Although, they are eukaryotes they are also defined as all eukaryotic organisms besides animals. Some examples of protists include slime molds, water molds, the unicellular animal-like prtozoa and amoeba. In 1990 protists merged with the fungi, plants, and animals to create the Eukarya "domain" of life. The purpose of doing this is to emphasize that the differences between plants, animals, fungi, and protists is much less than the difference between the eukaryotes and the bacteria and archaebacteria. The term "protist" derives from the greek protison, meaning the "first of all ones". Most have mitochondria, but some have later lost their and many also have chloroplast which help them carry out photosynthesis. Protists acquire food by extending their cellular membrane around a food particles and absorbing it. When the food is then in the cell wall, the protist then forms a food vacuole around the particle and begins digesting it. Many protists are also capable of eating bacteria. They are also capable of paralyzing a living bacterium once thay absorb it. There are three groups of protists which are fungi-like, plant-like, and animal-like, and the animal-like consists of flagellets, plant-like consists of algae. The fungi-like are however, less numerous. Source: http://www.wisegeek.com/what-are-protists.htm http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Protists.html