Biology

Review
(by some wiki material, Essential Cell Biology, and personal adds)

(May the force be with us)

1 Central Dogma of molecular biology and implications DNA contains the complete genetic information that defines the structure and function of an organism. Proteins are formed using the genetic code of the DNA. Three different processes are responsible for the inheritance of genetic information and for its conversion from one form to another: 1. Replication: a double stranded nucleic acid is duplicated to give identical copies. This process perpetuates the genetic information. 2. Transcription: a DNA segment that constitutes a gene is read and transcribed into a single stranded sequence of RNA. The RNA moves from the nucleus into the cytoplasm. 3. Translation: the RNA sequence is translated into a sequence of amino acids as the protein is formed. During translation, the ribosome reads three bases (a codon) at a time from the RNA and translates them into one amino acid In eucariotic cells, the second step (transcription) is necessary because the genetic material in the nucleus is physically separated from the site of protein synthesis in the cytoplasm in the cell. Therefore, it is not possible to translate DNA directly into protein, but an intermediary must be made to carry the information from one compartment to an other.

 Below a simple description of prokaryotic and eukaryotic cells

 Prokaryotic cells

Diagram of a typical prokaryotic cell: The prokaryote cell is simpler, and therefore smaller, than a eukaryote cell, lacking a nucleus and most of the other organelles of eukaryotes. There are two kinds of prokaryotes: bacteria and archaea; these share a similar structure. Nuclear material of prokaryotic cell consists of a single chromosome that is in direct contact with cytoplasm. Here, the undefined nuclear region in the cytoplasm is called nucleoid. A prokaryotic cell has three architectural regions: On the outside, flagella and pili project from the cell's surface. These are structures (not present in all prokaryotes) made of proteins that facilitate movement and communication between cells;

Enclosing the cell is the cell envelope generally consisting of a cell wall covering a plasma membrane though some bacteria also have a further covering layer called a capsule. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, serving as a protective filter. Though most prokaryotes have a cell wall, there are exceptions such as Mycoplasma (bacteria) and Thermoplasma (archaea). The cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and finally bursting (cytolysis) from osmotic pressure against a hypotonic environment. Some eukaryote cells (plant cells and fungi cells) also have a cell wall; Inside the cell is the cytoplasmic region that contains the cell genome (DNA) and ribosomes and various sorts of inclusions. A prokaryotic chromosome is usually a circular molecule (an exception is that of the bacterium Borrelia burgdorferi, which causes Lyme disease). Though not forming a nucleus, the DNA is condensed in a nucleoid. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular. Plasmids enable additional functions, such as antibiotic resistance.

Eukaryotic cells
Main article: Eukaryote

Diagram of a typical animal (eukaryotic) cell, showing subcellular components. Organelles: (1) nucleolus (2) nucleus (3) ribosome (4) vesicle (5) rough endoplasmic reticulum (ER) (6) Golgi apparatus (7) Cytoskeleton (8) smooth endoplasmic reticulum (9) mitochondria (10) vacuole (11) cytoplasm (12) lysosome (13) centrioles within centrosome

Eukaryotic cells are about 15 times wider than a typical prokaryote and can be as much as 1000 times greater in volume. The major difference between prokaryotes and eukaryotes is that eukaryotic cells contain membrane-bound compartments in which specific metabolic activities take place. Most important among these is a cell nucleus, a membrane-delineated compartment that houses the eukaryotic cell's DNA. This nucleus gives the eukaryote its

name, which means "true nucleus." Other differences include: 4. The plasma membrane resembles that of prokaryotes in function, with minor differences in the setup. Cell walls may or may not be present. 5. The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are associated with histone proteins. All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. Some eukaryotic organelles such as mitochondria also contain some DNA. 6. Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in chemosensation, mechanosensation, and thermosensation. Cilia may thus be "viewed as sensory cellular antennae that coordinate a large number of cellular signaling pathways, sometimes coupling the signaling to ciliary motility or alternatively to cell division and differentiation."[7] Eukaryotes can move using motile cilia or flagella. The flagella are more complex than those of prokaryotes. DNA Replication (Sum) Before a cell divides, its DNA is replicated (duplicated.) Because the two strands of a DNA molecule have complementary base pairs, the nucleotide sequence of each strand automatically supplies the information needed to produce its partner. If the two strands of a DNA molecule are separated, each can be used as a pattern or template to produce a complementary strand. Each template and its new complement together then form a new DNA double helix, identical to the original. Before replication can occurs, the length of the DNA double helix about to be copied must be unwound. In addition, the two strands

must be separated, much like the two sides of a zipper, by breaking the weak hydrogen bonds that link the paired bases. Once the DNA strands have been unwound, they must be held apart to expose the bases so that new nucleotide partners can hydrogen-bond to them. The enzyme DNA polymerase then moves along the exposed DNA strand, joining newly arrived nucleotides into a new DNA strand that is complementary to the template. Each cell contains a family of more than thirty enzymes to insure the accurate replication of DNA. Though DNA polymerase can elongate a polynucleotide strand by adding new nucleotides, it cannot start a strand from scratch because it can only bond new nucleotides to a free sugar (3') end of a nucleotide chain. DNA polymerase requires the assistance of a primer, a previously existing short strand of DNA (or RNA) that is complementary to the first part of the DNA segment being copied. This small strand of nucleotides anneals (binds) by complementary base pairing to the beginning of the area being copied. With the primer in place, DNA polymerase is then able to continue adding the rest of the pairs of the segment until a new double strand of DNA is completed. Primers are formed from free nucleotides in the cell by enzymes called DNA primases. That nucleotides can be added only to the sugar or 3' end of the growing complementary chain presents no problem for the side of the DNA chain opening at its phosphate or 5' end. The primer that binds to the first few exposed bases will end with a sugar (3') where the phosphate of a new nucleotide can be attached. From there on, DNA polymerase can continuously synthesize the growing complementary strand. This strand of DNA is called the leading strand.

A different challenge faces DNA polymerase when the complementary side of the DNA molecule begins unzipping from its sugar (3') toward its phosphate (5') end. A primer of complementary molecules attaching to the opening end of this chain would have a phosphate not a sugar at its exposed end so that new nucleotides could not be joined. To get around this problem, this strand is synthesized in small pieces backward from the overall direction of replication. This strand is called the lagging strand. The short segments of newly assembled DNA from which the lagging strand is built are called Okazaki fragments. As replication proceeds and nucleotides are added to the 3' end of the Okazaki fragments, they come to meet each other. The primer fragments are then booted out by enzymes and replaced by appropriate DNA nucleotides. The whole thing is then stitched together by another enzyme called DNA ligase.

Because human DNA is so very long (with up to 80 million base pairs in a chromosome) it unzips at multiple places along its length so that the replication process is going on simultaneously at hundreds of places along the length of the chain. Eventually these areas run together to form a complete chain. In humans, DNA is copied at about 50 base pairs per second. The process would take a month (rather than the hour it actually does) without these multiple places on the chromosome where replication can begin. DNA polymerase makes very few errors, and most of those that are made are quickly corrected by DNA polymerase and other enzymes that "proofread" the nucleotides added into the new DNA strand. If a newly added nucleotide is not complementary to the one on the template strand, these enzymes remove the nucleotide and replace it with the correct one. With this system, a cell's DNA is copied with less than one mistake in a billion nucleotides. This is equal to a person copying 100 large (1000 page) dictionaries word for word, and symbol for symbol, with only one error for the whole process! DNA Replication in eukaryotes: DNA replication in eukaryotes is much more complicated than in prokaryotes, although there are many similar aspects. Eukaryotic cells can only initiate DNA replication at a specific point in the cell cycle, the beginning of S phase. (the main difference is about the preparing phase in the cell cycle, the G1 phase, and some specialized proteins more than in the prokarya world) The eukaryotic chromosomes are contained within a nucleus that is bounded by a double-membrane nuclear envelope. Here the nucleolus and the nuclear fibrous skeleton can trigger and localize the genetic activities

Medical applications of DNA Replication ***Registrations were not clear at all, so I tried to dig the web to find the main medical applications of DNA Replication, but I can only make a list: Forensic studies Paternity test Genetical studies (to localize the part of the strand that rule an entire disease) History and anthropology (Using DNA measurement techniques to better understand our pasts) Nanotechnology (using DNA itself to develop interesting new physical concepts in the nano-world) Genetic Engineering (Using an understanding of genes to manipulate physical character traits) Transcription essentials Transcription is the process by which a DNA template is copied by RNA polymerase to produce a complementary molecule of RNA It involves four stages: 1. Binding of RNA polymerase to promoter sequences in the DNA template strand 2. Initiation of RNA synthesis 3. Elongation of RNA chain 4. Termination In the eukaryotic cells is more complex, one major difference is that eukaryotic cells have multiple forms of RNA polymerase that are specialized for synthesizing different types of RNA The three nuclear RNA polymerases recognize different families of DNA promoter seq. These eukaryotic promoters are usually bound by transcription factors

that associate with RNA polymerase rather than by RNA polymerase itself.
I dont want to lose time on transcription, just type transcription animation on youtube to get a quick look at this process Check on this site for further infos: http://users.rcn.com/jkimball.ma.ultranet/Bio logyPages/T/Transcription.html

Medical Applications of Transcriptions Protein synthesis is critical to the growth of cells; medicines that work by killing cells often target this process. A majority of antibiotics work by disrupting the translation process. Tetracycline is an antibiotic that inhibits the binding of tRNA to the assembly site. Streptomycin works by causing the translation process to make more mistakes than usualas high as one mistake for every 100 amino acids. Proteins with this many errors are not capable of performing their tasks, and the cells (in this case, bacteria) die. Streptomycin also inhibits the initiation of the synthesis process.
***I couldnt find more

Translation Protein Biosynthesis Essentials During translation, a small ribosomal subunit attaches to a mRNA molecule. At the same time, an initiator tRNA molecule recognizes and binds to a specific codon sequence on the same mRNA molecule. A large ribosomal subunit then joins the newly formed complex. The initiator tRNA resides in one binding site of the ribosome called the P site, leaving the second binding site, the A site, open. When a new tRNA molecule recognizes the next codon sequence on the mRNA, it attaches to the open A binding site. A peptide bond forms connecting the amino acid attached to the tRNA in the P site to the amino acid attached to the tRNA in the A binding site.

As the ribosome moves along the mRNA molecule, the tRNA in the P site is released and the tRNA in the A site is translocated to the P site. The A binding site becomes vacant again until another tRNA that recognizes the new mRNA codon takes the open position. This pattern continues as molecules of tRNA are released from the complex, new tRNA molecules attach, and the amino acid chain grows. The ribosome will translate the mRNA molecule until it reaches a termination codon on the mRNA.
***Watch a video, it is an easy process

Here some more Key-features of the mechanism: Translation involves initiation, elongation and termination stages During the initiation stage, initiation factors trigger the assembly of mRNA, ribosomal subunits, initiator aminoacyl tRNA into n initiation complex Chain elongation involves sequential cycles of aminoacyl tRNA binding, peptide bond formation and translocation, with each cycle driven by the action of elongation factors. The net result is that aminoacyl tRNAs add their amino acids to the growing polypeptide chain in an order specified by the codon sequence in mRNA Chain termination occurs when a stop codon in mRNA is recognized by release factors, which causes the mRNA and newly formed polypeptide to be released from the ribosome GTP binding and hydrolysis are required for the action of several initiation, elongation and release factors Proper folding of newly produced polypeptide chains is assisted by molecular chaperones. Abnormalities in protein folding can lead to various health problems, including Alzheimers disease and mad cow disease

Virus Generalities A virus is a small infectious agent that can replicate only inside the living cells of organisms. Most viruses are too small to be seen directly with a light microscope. Viruses infect all types of organisms, from animals and plants to bacteria and archaea. Since the initial discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, about 5,000 viruses have been described in detail, although there are millions of different types. Viruses are found in almost every ecosystem on Earth and are the most abundant type of biological entity. The study of viruses is known as virology, a sub-speciality of microbiology. Virus particles (known as virions) consist of two or three parts: the genetic material made from either DNA or RNA, long molecules that carry genetic information; a protein coat that protects these genes; and in some cases an envelope of lipids that surrounds the protein coat when they are outside a cell. The shapes of viruses range from simple helical and icosahedral forms to more complex structures. The average virus is about one one-hundredth the size of the average bacterium. The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids pieces of DNA that can move between cells while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity. Viruses spread in many ways; viruses in plants are often transmitted from plant to plant by insects that feed on the sap of plants, such as aphids; viruses in animals can be carried by blood-sucking insects. These disease-bearing organisms are known as vectors. Influenza viruses are spread by coughing and sneezing. Norovirus and rotavirus, common causes of viral gastroenteritis, are transmitted by the faecal-oral route and are passed from person to person by contact, entering the body in food or water. HIV is one of

several viruses transmitted through sexual contact and by exposure to infected blood. The range of host cells that a virus can infect is called its "host range". This can be narrow or, as when a virus is capable of infecting many species, broad. Viral infections in animals provoke an immune response that usually eliminates the infecting virus. Immune responses can also be produced by vaccines, which confer an artificially acquired immunity to the specific viral infection. However, some viruses including those causing AIDS and viral hepatitis evade these immune responses and result in chronic infections. Antibiotics have no effect on viruses, but several antiviral drugs have been developed. Key features: Structure: A virus particle, also known as a virion, is essentially a nucleic acid (DNA or RNA) enclosed in a protein shell or coat. Viruses are extremely small, approximately 15 - 25 nanometers in diameter. Genetic Material: Viruses may have double-stranded DNA, double-stranded RNA, single-stranded DNA or single-stranded RNA. The type of genetic material found in a particular virus depends on the nature and function of the specific virus. The genetic material is not typically exposed but covered by a protein coat. The viral genome can consist of a very small number of genes or up to hundreds of genes depending on the type of virus. Note that the genome is typically organized as a long molecule that is usually straight or circular.

Capsids The protein coat that envelopes viral genetic material is known as a capsid. A capsid is composed of protein subunits called capsomeres. Capsids can have several shapes: polyhedral, rod or complex. Capsids function to protect the viral genetic material from damage. In addition to the protein coat, some viruses have specialized structures. For example, the flu virus has a membrane-like envelope around its capsid. The envelope has both host cell and viral components and assists the virus in infecting its host. Capsid additions are also found in bacteriophages. For example, bacteriophages can have a protein "tail" attached to the capsid that is used to infect host bacteria. Virus Replication Viruses are intracellular obligate parasites which means that they cannot replicate or express their genes without the help of a living cell. A single virus particle (virion) is in and of itself essentially inert. It lacks needed components that cells have to reproduce. When a virus infects a cell, it marshals the cell's ribosomes, enzymes and much of the cellular machinery to replicate. Unlike what we have seen in cellular replication processes such as mitosis and meiosis, viral replication produces many progeny, that when complete, leave the host cell to infect other cells in the organism. Viruses may contain double-stranded DNA, double-stranded RNA, single-stranded DNA or single-stranded RNA. The type of genetic material found in a particular virus depends on the nature and function of the specific virus. The exact nature of what happens after a host is infected varies depending on the nature of the virus. The process for double-stranded DNA, single-stranded DNA, double- stranded RNA and single-stranded RNA viral replication will

differ. For example, double-stranded DNA viruses typically must enter the host cell's nucleus before they can replicate. Single-stranded RNA viruses however, replicate mainly in the host cell's cytoplasm. Once a virus infects its host and the viral progeny components are produced by the host's cellular machinery, the assembly of the viral capsid is a non-enzymatic process. It is usually spontaneous. Viruses typically can only infect a limited number of hosts (also known as host range). The "lock and key" mechanism is the most common explanation for this range. Certain proteins on the virus particle must fit certain receptor sites on the particular host's cell surface. How Viruses Infect Cells The basic process of viral infection and virus replication occurs in 6 main steps. 1. Adsorption - virus binds to the host cell. 2. Penetration - virus injects its genome into host cell. 3. Viral Genome Replication - viral genome replicates using the host's cellular machinery. 4. Assembly - viral components and enzymes are produced and begin to assemble. 5. Maturation - viral components assemble and viruses fully develop. 6. Release - newly produced viruses are expelled from the host cell. Viruses may infect any type of cell including animal cells, plant cells and bacterial cells. To view an example of the process of viral infection and virus replication, see Virus Replication: Bacteriophage. You will discover how a bacteriophage, a virus that infects bacteria, replicates after infecting a bacterial cell.

Amendments to the Central Dogma

I could not find anything about this, the only interesting and faithfully information about the dogma are those processes not stated by itself but still true in the real practice:

Reverse transcription is the transfer of information from RNA to DNA (the reverse of normal transcription). RNA replication is the copying of one RNA to another. Many viruses replicate this way. Direct translation from DNA to protein has been demonstrated in a cell-free system (i.e. in a test tube), using extracts from E. coli that contained ribosomes. Variation in methylation states of DNA can alter gene expression levels significantly. Prions are proteins that propagate themselves by making conformational changes in other molecules of the same type of protein.

Im sure I could not reach the end of the entire work this time but as the last one, I hope it would be helpful for You guys Your beloved and tired and crazy and emotional and complicated and lazy and excited and strange and pretty and adorable colleague,

Alessandro Motta

PS: it will be more complicated than what we can think, if theres a hell below. We are all gonna go!