sometimes the heart

Minggu, 16 Desember 2012


What are xenobiotics?

Most of the ingested material and compounds are foods and drugs. Some of these cannot be utilized by the body as foods. These may be harmful if they accumulated in cells, as they have no metabolic function. These are called xenobiotics.

Where does the term xenobiotic come from?

The tem xenobiotic is derived from Greek words “xenos” meaning foreigner, stranger and “bios” meaning life added to the Greek suffix for adjectives “tic”.

Examples of xenobiotics

Xenobiotics include:
  • synthetic drugs
  • natural poisons
  • food additives
  • environmental pollutants
  • antibiotics etc.
More than 200,000 xenobiotics have been identified and these are metabolized and detoxified by xenobiotic-metabolizing enzymes.

Xenobiotic metabolism

In humans xenobiotics are metabolized by cytochrome P450 oxidases, UDP-glucuronosyltransferases, and glutathione ''S''-transferases. These enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The molecules from phase II that are water-soluble are then pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III).

Two major phases of xenobiotic metabolism

Metabolism of xenobiotics thus occurs in two major phases.
Phase I
This process is characterized by hydroxylation. This is carried out by a variety of monooxygenases, also known as cytochrome P450s. These Cytochrome P450s catalyze reactions that introduce one atom oxygen delivered from molecular oxygen into the substrate, yielding a hydroxylated product.
Phase II
In this phase the hydroxylated species are conjugated with a variety of hydrophilic compounds such as glucuronic acid, sulfate or gluthione. This makes the compounds water soluble that can be easily eliminated from the body.

Xenobiotics and oxidative stress

A related problem for aerobic organisms is oxidative stress caused by reactive oxygen free radicals. Oxidative stress is a large increase in the cellular reduction potential, or a large decrease in the reducing capacity of the cellular redox couples. This process involves formation of disulfide bonds during protein folding that leads to production of reactive oxygen species such as hydrogen peroxide.
Free radicals cause a chain reactions leading to consecutive oxidation. These radicals attack molecules like fat, protein, DNA, sugar etc.
Free radicals are removed by antioxidant metabolites such as glutathione and enzymes such as catalases and peroxidases. Antioxidants neutralize free radicals before they can attack cell proteins, lipids and carbohydrates. They inhibit and delay the oxidative process.
Reviewed by April Cashin-Garbutt, BA Hons (Cantab)



Metabolism is a term that is used to describe all chemical reactions involved in maintaining the living state of the cells and the organism. Metabolism can be conveniently divided into two categories:
  • Catabolism - the breakdown of molecules to obtain energy
  • Anabolism - the synthesis of all compounds needed by the cells
Metabolism is closely linked to nutrition and the availability of nutrients. Bioenergetics is a term which describes the biochemical or metabolic pathways by which the cell ultimately obtains energy. Energy formation is one of the vital components of metabolism.

Nutrition, metabolism and energy

Nutrition is the key to metabolism. The pathways of metabolism rely upon nutrients that they breakdown in order to produce energy. This energy in turn is required by the body to synthesize new proteins, nucleic acids (DNA, RNA) etc.
Nutrients in relation to metabolism encompass bodily requirement for various substances, individual functions in body, amount needed, level below which poor health results etc.
Essential nutrients supply energy (calories) and supply the necessary chemicals which the body itself cannot synthesize. Food provides a variety of substances that are essential for the building, upkeep, and repair of body tissues, and for the efficient functioning of the body.
The diet needs essential nutrients like carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur, and around 20 other inorganic elements. The major elements are supplied in carbohydrates, lipids, and protein. In addition, vitamins, minerals and water are necessary.

Carbohydrates in metabolism

Foods supply carbohydrates in three forms: starch, sugar, and cellulose (fiber). Starches and sugars form major and essential sources of energy for humans. Fibers contribute to bulk in diet.
Body tissues depend on glucose for all activities. Carbohydrates and sugars yield glucose by digestion or metabolism.
The overall reaction for the combustion of glucose is written as:
C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + energy
Most people consume around half of their diet as carbohydrates. This comes from rice, wheat, bread, potatoes, pasta, macaroni etc.

Proteins in metabolism

Proteins are the main tissue builders in the body. They are part of every cell in the body. Proteins help in cell structure, functions, haemoglobin formation to carry oxygen, enzymes to carry out vital reactions and a myriad of other functions in the body. Proteins are also vital in supplying nitrogen for DNA and RNA genetic material and energy production.
Proteins are necessary for nutrition because they contain amino acids. Among the 20 or more amino acids, the human body is unable to synthesize 8 and these are called essential amino acids.
The essential amino acids include:
  • lysine
  • tryptophan
  • methionine
  • leucine
  • isoleucine
  • phenylalanine
  • valine
  • threonine
Foods with the best quality protein are eggs, milk, soybeans, meats, vegetables, and grains.

Fat in metabolism

Fats are concentrated sources of energy. They produce twice as much energy as either carbohydrates or protein on a weight basis.
The functions of fats include:
  • helping to form the cellular structure;
  • forming a protective cushion and insulation around vital organs;
  • helping absorb fat soluble vitamins,
  • providing a reserve storage for energy
Essential fatty acids include unsaturated fatty acids like linoleic, linolinic, and arachidonic acids. These need to be taken in diet. Saturated fats, along with cholesterol, have been implicated in arteriosclerosis and heart disease.

Minerals and vitamins in metabolism

The minerals in foods do not contribute directly to energy needs but are important as body regulators and play a role in metabolic pathways of the body. More than 50 elements are found in the human body. About 25 elements have been found to be essential, since a deficiency produces specific deficiency symptoms.
Important minerals include:
  • calcium
  • phosphorus
  • iron
  • sodium
  • potassium
  • chloride ions
  • copper
  • cobalt
  • manganese
  • zinc
  • magnesium
  • fluorine
  • iodine
Vitamins are essential organic compounds that the human body cannot synthesize by itself and must therefore, be present in the diet. Vitamins particularly important in metabolism include:

Metabolic pathways

The chemical reactions of metabolism are organized into metabolic pathways. These allow the basic chemicals from nutrition to be transformed through a series of steps into another chemical, by a sequence of enzymes.
Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy. These reactions also are coupled with those that release energy. As enzymes act as catalysts they allow these reactions to proceed quickly and efficiently. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells.
Reviewed by April Cashin-Garbutt, BA Hons (Cantab)


  1. http://www.unm.edu/~lkravitz/Article%20folder/Metabolism.pdf
  2. http://www.biobreeders.com/images/Nutrition_and_Metabolism.pdf
  3. http://www.oup.com/us/static/companion.websites/9780199730841/McKee_Chapter8_Sample.pdf
  4. http://cronus.uwindsor.ca/units/biochem/web/biochemi.nsf/18e8732806421826852569830050331b/7a371e9af805f74e85256a4f00538021/$FILE/Energy%20metabolism.pdf
  5. http://www.elmhurst.edu/~chm/vchembook/5900verviewmet.html

Selasa, 11 Desember 2012

What is Taxonomy and Where Did it Originate?

Taxonomy is the method by which scientists, conservationists, and naturalists classify and organize the vast diversity of living things on this planet in an effort to understand the evolutionary relationships between them. Modern taxonomy originated in the mid-1700s when Swedish-born Carolus Linnaeus (also known as Carl Linnaeus or Carl von LinnĂ©) published his multi-volume Systema naturae, outlining his new and revolutionary method for classifying and, especially, naming living organisms. Prior to Linnaeus, all described species were given long, complex names that provided much more information than was needed and were clumsy to use. Linnaeus took a different approach: he reduced every single described species to a two-part, Latinized name known as the “binomial” name. Thus, through the Linnaean system a species such as the dog rose changed from long, unwieldy names such as Rosa sylvestris inodora seu canina  and Rosa sylvestra alba cum rubore, folio glabro to the shorter, easier to use Rosa canina. This facilitated the naming of species that, with the massive influx of new specimens from newly explored regions of Africa, Asia, and the Americas, was in need of a more efficient and usable system.
Although trained in the field of medicine, botany and classification were the true passions of Linnaeus and he actively explored northern Europe and described and named hundreds of new plant species during his lifetime. As well, Linnaeus spent a great deal of time describing and naming new plant specimens that were sent to him from around the world by other botanists, including from the newly explored regions of the New World. Linnaeus classified this multitude of new plant species based upon their reproductive structures, a method which is still largely in use today.  In fact, the majority of the species described by Linnaeus are still recognized today, indicating how far ahead of his time he truly was. Although somewhat rudimentary by today’s standards, Linnaeus’ methods of describing species in such a way as to represent the relationships between them changed the face of taxonomy and allowed biologists to better understand the complex natural world around us.


What is a Biome? 
   A biome is a large area with similar flora, fauna, and microorganisms.  Most of us are familiar with the tropical rainforests, tundra in the arctic regions, and the evergreen trees in the coniferous forests. Each of these large communities contain species that are adapted to its varying conditions of water, heat, and soil.  For instance, polar bears thrive in the arctic while cactus plants have a thick skin to help preserve water in the hot desert.  To learn more about each of the major biomes, click on the appropriate heading to the right. 
What is an Ecosystem? 
   Most of us are confused when it comes to the words ecosystem and biome.  What's the difference?  There is a slight difference between the two words.  An ecosystem is much smaller than a biome.  Conversely, a biome can be thought of many similar ecosystems throughout the world grouped together.  An ecosystem can be as large as the Sahara Desert, or as small as a puddle or vernal pool. 
   Ecosystems are dynamic interactions between plants, animals, and microorganisms and their environment working together as a functional unit.  Ecosystems will fail if they do not remain in balance.  No community can carry more organisms than its food, water, and shelter can accomodate.  Food and territory are often balanced by natural phenomena such as fire, disease, and the number of predators.  Each organism has its own niche, or role, to play. 
 How have humans affected the ecosystems? 
   We have affected ecosystems in almost every way imaginable!  Every time we walk out in the wilderness or bulldoze land for a new parking lot we are drastically altering an ecosystem.  We have disrupted the food chain, the carbon cycle, the nitrogen cycle, and the water cycle.  Mining minerals also takes its toll on an ecosystem.  We need to do our best to not interfere in these ecosystems and let nature take its toll.

Sabtu, 01 Desember 2012

heart and circulation of snail.

Scheme of the circulation:

H = Head - cephalic hemocoel
F = Foot hemocoel
E = Oesophagus
Vm= Visceral mass (hemocoel)
aK = anterior (front) Kidney
pK = posterior (back) Kidney
A = Ampulla
Au = Auricle
V = Ventricle
Aa = Aorta anterior
Ap = Aorta posterior
vS = Visceral sinus
fS = Foot sinus

The blood circulation of the apple snail is a typical example of the circulation in a monocardia: there is only one auricle that receives oxygen rich blood from the lung and the gills and deoxygenated blood from the kidney. So there is no separated blood circulation for oxygen rich and deoxygenated blood like in mammals and birds. It's a less efficient system, but it fulfils the needs of a snail very well.
The blood of apple snails (and snails in general) has two functions: transport of O2, CO2, hormones, nutrition and waste products and a structural function: a hydroskeleton.
The transport capacity of the blood  for O2 and CO2 is enhanced by the chemical substance hemocyanine in the blood cells. Hemocyanine fulfils the same function as haemoglobin does in mammals (binding O2 and CO2 to ease transportation), but is colourless in contrary to the red colour of haemoglobin.
As the body of a snail does not contain a skeleton to support the extension movements, for example stretching out a tentacle, snails have to use another way: regulating the blood pressure in the body parts. In other words: inflating and deflating parts of the body in combination of muscle contraction to change shape. The regulation of the local blood is obtained by controlling the input and output of the bloodflow by contracting and relaxing small muscles that surround the veins.
Retracting movements are done by simple muscle contraction, without the need of fluid transportation.


Snail heart in action:

The transport of the blood to and from the organs occurs through arteries (from heart to organs) and veins (from organs to heart). Snails don't have capillary veins and arterioles, which means their blood doesn't flow within tube-like structures (veins and arteries) during the whole circulation, but at the tissue level the blood circulates free between the cells and structures embedded in blood cavities (hemocoels) within the body (= open circulation).
The circulation and filtration of the blood:
The heart of apple snails is well developed and consists of two chambers: the auricle and the ventricle.
The auricle is which receives the blood influx from the lung and the kidney veins is much smaller then the ventricle. Inside the auricle, there are many small muscle fibres connecting the opposite wall trough the lumen. The walls have a spongy surface at the inside and a basal layer at the outside. The blood is able to reach the basal membrane through the spongy surface. Contraction is achieved by contracting these muscle fibres.
The ventricle is much larger and has thick, muscular walls with many spaces between the wall muscles, allowing the blood to be trapped in these semi-vescicles and filtered through the basal membrane. In contrast with the auricular contraction, the ventricular contraction is based on contraction of the wall muscles. The mean ventricular pulse pressure of the African apple snail Lanistes carinatus is reported to be around 7.8 cm of water.
The aortic ampulla functions as a compensation sac and compensates the elevated blood pressure in the aorta during the contraction of the ventricle. Besides its function to regulate the blood pressure, the ampulla also has a function in the immune system as the walls of the ampulla consists of vacuolated tissue with many phagocytes in it. These phagocytes possibly eliminate micro-organisms from the bloodflow. The wall of the ampulla is relatively impermeable, excluding the ampulla for blood filtration.
Both the heart and the ampulla are embedded in the pericard, which is connected with the posterior kidney through a renopericadial canal. The walls of the pericard cover the heart and the ampulla and in the pericard cavity the walls are covered with microvilli, small intercellular channels and ridges. Near the renopericardial canal there are some mucous cells secreting mucus, presumably to bind small particles to be transported to the kidney.
The fluid excreted in the pericard cavity can be considered to be primary urine and this fluid is transported to the kidneys for further filtration and resorption of usable compounds (sodium and chlorine).
The kidney or nephridium consists of two parts: the posterior chamber which excretes uric acid and purines and the anterior chamber which has osmoregulatory function.

The posterior kidney chamber receives the primary urine from the pericard cavity. The folds on the posterior chamber wall have a dense vascular network and are covered with excretory, ciliated and mucous cells. The excretory cells excrete uric acids and other purines from the blood into the lumen of the chamber in which the primary urine flows.
The anterior kidney chamber differs from the posterior chamber in that the lumen is occluded with large lamina that covers the walls. These lamina remarkably increase the surface area that comes in contact with the urine. The epithelium on these lamina is almost entirely consisting of resorptive cells that presumable resorb ions from the urine into the blood.
The renal aperture (urine opening) is situated in the upper region of the right mantle cavity. The urine produced by the kidneys is expelled here.
The aorta with it's white calcareous granula in it's wall consists two parts: the anterior and the posterior part.
The anterior aorta connects the heart with the head (cephalic hemocoel) and the foot (foot hemocoel), while the posterior aorta divides close to the heart with one artery distributing the blood to the digestive system and the second serves several other organs (testis, ovaria, intestines etc.).
After circulating through the tissues and hemocoels of the snail, the blood is collected in large veins and brought to the posterior kidney.
A portion of the blood that enters the posterior kidney directly flows back to the heart, while the remaining blood enters the vascular system of the kidneys (posterior and anterior part).
After passing the anterior kidney, the blood flows through the mantle vein, from where many small veins bring the blood to the gills and the lung, where O2 uptake and CO2 is exchange takes place.
The lung-gill vein collects the oxygen rich blood from the lung and the gills and brings it back to the heart. 

copy right :  http://www.applesnail.net/content/anatomy/circulation.php



Selasa, 27 November 2012

Biogeochemical Cycles

There are a few types of atoms that can be a part of a plant one day, an animal the next day, and then travel downstream as a part of a river’s water the following day. These atoms can be a part of both living things like plants and animals, as well as non-living things like water, air, and even rocks. The same atoms are recycled over and over in different parts of the Earth. This type of cycle of atoms between living and non-living things is known as a biogeochemical cycle.
All of the atoms that are building blocks of living things are a part of biogeochemical cycles. The most common of these are carbon and nitrogen.

Tiny atoms of carbon and nitrogen have no legs to walk, no bicycles, cars, or airplanes. Yet they can travel around the world as a part of biogeochemical cycles. So, how do these little things move around the planet? Here’s an example: An atom of carbon is absorbed from the air into the ocean water where it is used by little floating plankton doing photosynthesis to get the nutrition they need. There is the possibility that this little carbon atom becomes part of the plankton’s skeleton, or a part of the skeleton of the larger animal that eats it, and then part of a sedimentary rock when the living things die and only bones are left behind. Carbon that is a part of rocks and fossil fuels like oil, coal, and natural gas may be held away from the rest of the carbon cycle for a long time. These long-term storage places are called “sinks”. When fossil fuels are burned, carbon that had been underground is sent into the air as carbon dioxide, a greenhouse gas.
Recently, people have been causing these biogeochemical cycles to change (see links below). When we cut down forests, make more factories, and drive more cars that burn fossil fuels, the way that carbon and nitrogen move around the Earth changes. These changes add more greenhouse gases in our atmosphere and this causes more global warming.

copy : http://www.windows2universe.org/earth/Life/biogeochem.html

Minggu, 25 November 2012



Ribosomes are tiny particles, about 200 A. It is composed of both proteins and RNA; in fact it has approximately 37 - 62% RNA, and rest are made up of proteins. The RNA present in ribosomes are obviously called ribosomal RNA, and they are produced in the nucleolus, which is a prominent globular structure in the nucleus. Thus, the proteins are gene products of themselves, and one ribosome is made up of dozens of genes. The ribosomes fall into two categories: Those that are free to roam in the cytoplasm , and those that are bound to gigantic, cobwebby organelles made up of membranes, called the endoplasmic reticulum; thus, causing a rough surface. Although, the two kinds of ribosomes play similar roles in translating mRNA to produce proteins, they are very distinct in where its product is located. The ribosomes in the cytoplasm allows its protein to roam about freely, while the bound ribosomes transfer their functional protein into the endoplasmic reticulum. In addition, ribosomes are also located within the mitochondria, and the chloroplast, but are only few in content. Click Here This spherical particle of 23nm, is composed of two subunits; a large and small  In Eukaryotes, the co-efficient of ribosomes are 80s, of which is divided into 60s for the large, and 40s for the small subunit. The 60s contain 28s rRNA, with a small fragment that is attached noncovalently and can be released upon heating; a 5.8s, and a very small - 120 nucleated of 5sRNA. Whereas, the 40s subunit has only a single 18s rRNA . In prokaryotes, however, the large and small subunits are split into 50s and 30s, making a total of 70s respectively. The 50s has two types of rRNA - a 23s and a 5s . It also has 32 different proteins. On the other hand, the 30s contains a single 16s rRNA  plus, 21 different types of proteins Label. To help better understand what the s stands for in rRNA, let us use the prokaryotes as an example. The 50s and 30s refers to the sedimentation coefficient of the two subunits. This coefficient is a measure of the speed with which the particles sediment through a solution when spun in an ultra centrifuge. Thus, the particles with larger coefficient would centrifuge and settle much faster since it is has more mass than the particle with the smaller coefficient. 50s + 30s =======> 70s Note that the two subunits above make up the entire ribosomal molecule which is 70s. The reason the coefficients do not add up is because they are not proportional to the particle weight. During protein synthesis, ribosomes line up along the mRNA and form a polysome, also called the polyribosome. The mRNA is aligned in the gap between the 2 ribosomal subunits. It is possible that the nascent peptide chain grows through a channel or groove in the large ribosomal subunit. This is predicted to be the case since ribosomes protect a segment of 30-40 amino acids from degradation. Speaking of amino acids, up to 30 ribosomes can attach on one strand of mRNA to form amino acid chains thus leading to protein formation. Ribosomes act as the backbone for many molecules during translation. It provides room for many structures to situate itself thus enhancing protein synthesis. For example, mRNA inserts itself between the two subunits; the peptidyl transferase complex - the enzyme that allows for the tRNA to break apart from the amino acid on P-site; this enzyme lays across the molecule, between the subunits. It contains the P and the A-site for tRNA binding. Last but not least, the ribosome molecule allows the growing polypeptide chain, to emerge from the back of the structure, thus it is situated perpendicular to the mRNA chain. Ribosomes have a tertiary structure. Ribosomes make up a large part of cells in many species, which leads to protein manufacturing. For example, in E.Coli (bacteria), they make up about 1/4 of the total cell mass. They are intensely basiphilic (having high affinity for bases). Due to its complex structures, with many proteins and different kinds of RNA, researchers have found it very difficult to study the macro molecular structure of ribosomes, especially for the fact it is quite impossible to observe its crystal using an x-ray diffraction. Thus, scientists have been forced to use other means of study to map the proteins and RNA components in ribosome. Some of these are the cross-linking, immunoelectron microscopy, and low-angle neutron scattering methods. The cross-linking shows the protein arrangement and the types of bonds it forms within itself. The neutron scattering experiments forms horizontal lines that show the entire structure of ribosome, with its two subunits, and shows where the proteins are arranged in the molecule. The empty regions around the proteins is where the rRNA is located. The immunoelectron microscopy, shows the proposed location of the 16s rRNA molecule of the small subunit, in prokaryotes.


The ribosomes plays a very important role in protein synthesis, which is the process by which proteins are made from individual amino acids. Without the ribosomes the message would not be read, thus proteins could not be produced. Therefore, ribosomes play a very important role in role in protein synthesis. The primary agent in the process of translating the mRNA into a specific amino acid chain is the ribosome, which consists of two subunits. These subunits are made up of a third and extremely abundant type of RNA, ribosomal RNA (rRNA), and together contain up to eighty-two specific proteins assembled in a precise sequence.The ribosomes constituents must be put together in an extremely precise position and sequence. This assembled ribosome displays a series of small groves, tunnels, and platforms, where the action of protein synthesis occurs .There are the active sites, each dedicated to one of the tasks required for translation of mRNA into protein. Proteins being synthesized for export out of the cell, are made by ribosomes attached to the rough endoplasmic reticulum. In contrast, proteins for use by the cell are generally made in the cytoplasm by free ribosomes. Several of these free ribosomes may attach to a single mRNA molecule, giving rise to the polyribosome or polysome. Protein synthesis takes place on polyribosomes (or polysomes) where 80S ribosomes associate with an mRNA coding for a given protein. The number of ribosomes associated in the polysomal chains depends on the size of the mRNA. This is also associated with the size of the protein that is being synthesized. Outside the polyribosome, the ribosomes are dissociated and form a pool of free subunits. Transfer RNAs are also bound to the ribosome. There are quite a few factors involved in the formation of the initiation complex. These include: GTP, methionine tRNA, an initiation codon in mRNA, 80S ribosomes, and three protein factors . The process of protein synthesis begins with the capture of the tRNA, which is carrying an amino acid, by an initiation factor. This binds to a small ribosomal subunit, which occupies one of the active sites in the ribosomes, the P (protein) site. This initiation complex recognized and binds to the 5' end of an mRNA molecule and slides down to the initiation codon, which is always an AUG sequence of amino acids. The large subunit of the ribosome now joins the complex. A second tRNA is now brought into the ribosome by the elongation factor. If the anticodon of the tRNA pairs with the next codon of the message, the tRNA occupies the A (acceptor) site on the ribosome. This positions the second amino acid adjacent to the initiation methionine. Then an enzyme, peptidyl transferase, which is part of the large ribosomal subunit mediates the separation of the first amino acid from its tRNA and the formation of a peptide bond between the initial methionine and the amino acid is formed. The P site is now occupied by an uncharged tRNA molecule . The ribosome will now move down the mRNA by one codon, a process known as translocation. This movement shifts the growing polypeptide chain to the P position, and results in an empty A site, where a new charged tRNA can enter and pair, by forming a hydrogen bond between the codon and the anticodon. This holds the tRNA into place long enough for an even more stable binding to occur. The uncharged tRNA that previously occupied the P site is booted out of the ribosome and will be recharged and recycled by the cell. The energy needed for this process is supplied by the hydrolysis of guanosine triphosphate (GTP). The process then continues along the length of the mRNA, until the first stop codon is encountered. At that point the action of a termination factor releases the completed protein from the last tRNA and the ribosome dissociates into its component parts. Another function of the ribosomes occurs in the relation to the neuron and axons. The cell body of a typical large neuron contains vast numbers of ribosomes. Although dendrites often contain some ribosomes, there are no ribosomes in the axon, and its protein must therefore be provided by the many ribosomes in the cell body. To see the process of protein synthesis