There are different types of Amino acids; but this article refers to the Amino acids needed for protein synthesis in the human body. Amino acids are the building blocks of polypeptide chains which are the building blocks of protein. The human body uses 20 different amino acids in our genetic code. In most cases, our bodies can manufacture 11 of the 20 amino acids used to build protein molecules, but we need to derive the other 9 amino acids from our diet. These 9 that cannot be synthesized without nutrients in our food are called Essential Amino acids. They include the following list with a selection of foods they can be found in. The list of foods is in no way to be considered comprehensive or exhaustive (as I am not a medical professional), but rather a sampling of the foods that these amino acids can be found in.

Isoleucine – found in eggs, soy protein, seaweed, turkey, chicken, lamb and cheese

Leucine – found in soy protein concentrate, peanuts, wheat germ, almonds, lentils, chick peas, corn and brown rice

Lysine – found in soy, red meat, lamb, poultry, cheese, certain fish and eggs

Methionone – sesame seeds, Brazil nuts, fish and cereal grains

Phenylalanine – dried egg white powder, dried whole egg powder, peanut flour, seeds, soy flour, soy meal, some fish, frozen tofu, and cheese. An important non-food source is Aspartame.

Threonine – cottage cheese, poultry, fish, meat and lentils

Tryptophan – chocolate, oats, dried dates, milk, yogurt, cottage cheese, red meat, eggs, fish, and poultry

Valine – cottage cheese, fish, poultry, peanuts, sesame seeds and lentils

Histidine – soy protein isolate,dried egg white, parmesean cheese, sesame flour, peanut flower, dried frozen tofu, defatted soy flour.

There are two provisionally needed amino acids that some people cannot manufacture without dietary sources. Tyrosine can be manufactured from Phenylalanine, but in individuals suffering from PKU – an inability to digest Phenylalanine, Tyrosine may be deficient. Secondly, Selenocysteine, is an unclassified Amino acid that may be deficient in some populations.

Lithograph of the Rotator Cuff group from Gray's Anatomy.

The Rotator Cuff is a group of four muscles that attach to the humerus and scapula to support the shoulder joint. The Glenohumeral joint (where the scapula and humerus meet, a.k.a. the shoulder) is a ball and socket style joint and due to the small surface area of each bone where they connect, it is the most moveable joint in the entire body. The Rotator Cuff along with deltoid, teres major and the coracobrachialis make up the 7 muscles responsible for the movement and stability in the shoulder.

The four muscles of the Rotator Cuff include the supraspinatus, the subscapularis, infraspinatus and teres minor all of which have their attachment and/or insertion points on the scapula bone and/or the humerus (the large bone connecting the shoulder to the elbow). The most commonly damaged muscles in the group are the supraspinatus and the infraspinatus.

A sudden, powerful movement of the shoulder joint can cause an acute tear. Bowlers, tennis players, boxers, and pitchers often suffer an acute tear. A chronic tear is caused by repetitive motion wearing down the muscle on or near the tendon. Chronic tears can lead to Impingement Syndrome; the condition where the inflammed muscles are squished under the acromial arch before they attach to the Humerus. Chronic tears occur most often in people over 40 years old.

Rotator Cuff tears have a 40-90% treatment success rate.

Smooth Muscle cells by Polarlys

The human body has three different kinds of muscle: smooth, skeletal and cardiac. Smooth muscle is the involuntary, non striated muscle that is found in your digestive tract, blood vessels, lymph system, bladder, respiratory system, uterus, skin – almost any part of the body you can think of that requires movement of some type that is automatically regulated without your conscious control. For example, smooth muscle lines your digestive tract and is responsible for moving the partially digested food through the small and large intestine by peristalsis, the systematic contraction and relaxation of muscle fibers that produces a squeezing effect. Peristalsis is what happens when you swallow food as well. Smooth muscle cells contain only one nucleus; whereas skeletal muscle cells contain multiple nuclei.

Skeletal muscle is under our conscious control and is involved in every movement the human body

Skeletal muscle structure by Raul654

makes; be it walking, talking, chewing, riding a bike, and so on. Skeletal muscle fibers are structurally different from smooth muscle in that they are striated – under a microscope, dark lines appear along their length. Each space between two striations in a skeletal muscle cell is called a sarcomere and is made up of actin and myosin proteins. When a muscle contracts or relaxes, actin and myosin fibers slide against one another becoming closer together or further apart. Thus the striations appear (if we could see this in action under a microscope) to come closer together or further apart.

Individual smooth muscle cells are fusiform in shape and flatten out in their relaxed state and fatten up in their contracted state. Individually, these cells have more elasticity than skeletal muscle cells.

Heart Muscle fibers by Dr.S. Girod, Anton Becker

Cardiac muscle cells are striated, involuntary cells found in the heart. They differ from skeletal and smooth muscle in many ways, but two are key: cardiac muscle fibers appear branched under the microscope, but still have a striated appearance and the chemical mechanisms that activate their contraction or relaxation are different from those of skeletal or smooth muscle.

Rafflesia arnoldii Photo credit ma_suska

The biggest flower in the world is the Rafflesia arnoldii, a.k.a. the Corpse Flower, so named because when blooming, it smells of rotting flesh. This flower is unusual in design in that it appears to have no stems, leaves or roots. The Rafflesia arnoldii grows as a parasite on the Tetrastigma vine. This flower takes over a  year to blossom, and sadly, is an endangered species. It lives in the rainforests of Sumatra, Indonesia and Malaysia and its habitat is disappearing such that scientists don’t know how many of this plant are left.

The Rafflesia arnoldii is a non-photosynthetic plant; it gathers all the nutrients it needs for growth from the Tetrastigma vine. The Corpse flower blooms to over a meter wide and can weigh up to 11 kg. The stench of rotting meat attracts flies and beetles for pollination. This flower not only smells like a rotting corpse, it looks like flesh as well; with large, blood red petals with white spots.

The Rafflesia arnoldii bud has been eaten as a delicacy in Thailand. It is used in some parts of Malaysia to aid women after childbirth, to staunch bleeding and shrink the uterus, although the chemical properties haven not been extensively studied; so any health claims have not been verified. It may even be toxic as it contains tannin and phenol. Rafflesias have also been used in religious ceremonies.

Cow Pox pustules on a Cow's Udder

Both viruses and bacteria cause diseases in plants and animals. It’s important to note, though, the vast majority of bacteria are harmless to humans, and a great number of bacteria are essential to our survival. Viruses, bacteria, prions and fungus that cause disease are known as pathogens. Pathogens are simply infectious agents; as the word origin suggests in this case: “pathos” means suffering and “gen” means the generation of.  A virus is an interesting entity that hovers on the cusp of being life. It is basic genetic material boiled down to the most essential elements: genes, protein and sometimes, a lipid outer shell, built using the host’s cellular material. That’s it. Bacteria are prokayotic cells, of which there are many, many varieties. Prokaryotes lack a nucleus and have very few (if any) membrane bound organelles (cellular organs wrapped in their own individual coating).

A virus cannot multiply on its own; it needs to be inside a cell in order to divide. Typically, a virus is proliferated in the following manner: first, it attaches to the outer shell of a cell and either through diffusion or chemical messenger channels, is absorbed. Next, the protein covering protecting the viral DNA or RNA (there are both DNA and RNA viruses) dissolves, releasing the virus’ genetic material. The plant, animal, or fungi cell then combines its own DNA with the viral DNA and begins making copies. Since the viral DNA is actually combined with the host’s DNA, any host cell division will also make a copy of the virus. Viruses can also proliferate by cellular lysis: the host cell completely fills up with copies of the virus, causing the cell to burst and spew out viruses which can then infect other cells in the body. The perfect parasite!

Now the biggest, medically relevant difference between viruses and bacteria is how they are treated when infecting a body. Antibiotics only treat bacterial infections; not viral ones; like the Common Cold or Influenza. Your body needs to just batten down the hatches and kill the viral invaders on its own. It has only been very recently that drugs have been developed to treat a virus once it has become symptomatic: Tamiflu and Relenza are but a few. The main defense against viruses is still vaccines: altered forms of the virus introduced to the body to create an immunity “memory”. Our body then recognizes subsequent exposures to the same virus and can mobilize an immune attack accordingly. The etching at the right is Cow Pox, the much less dangerous form of a similar strain called Small Pox. It was discovered that those who were exposed to Cow Pox, did not succumb to Small Pox as the Cow Pox created an immunity memory.

Typical Plant Cell

The biggest difference between plant cells and animal cells is that plant cells have a cell wall surrounding their cell membrane. Animal cells have no such wall. This gives plant cells rigidity and allows them to remain upright. Plant cells have a large vacuole that takes up most of the room inside their membrane. The vacuole controls the movement and storage of nutrients and waste within the cell, and helps maintain the cell’s structure using fluid for support. Plant cells are relatively uniform in structure – they are all roughly the same shape. whereas there are many different kinds, sizes and shapes of animal cells. Plant cells also contain chloroplasts; the organelles that make food needed for the plant’s growth, using sunlight to convert carbon dioxide and water into sugar and oxygen in a process known as photosynthesis (meaning to synthesize using light). The oxygen biproduct of photosynthesis allows Earth to be inhabited by air breathing organisms; simply put, plants make air for us to breathe. Plant cells have plasmodesmata; pores in the cell wall that allow chemical communication between cells.

Typical Animal Cell

Animal cell membranes have all sorts of receptor proteins that become activated to trigger an opening in the membrane to allow hormones, nutrients and waste to move into and out of the cell. Some substances, such as water can diffuse through the cell wall without needing a chemical signal to do so.

Trash Island, also known as the Great Pacific Garbage Patch or the Pacific Trash Vortex is an area in the north, central Pacific Ocean with high concentrations of garbage debris, made up primarily of plastic. This patch of debris is estimated to be between 0.41% to 8.1% the size of the Pacific Ocean. An exacts size is almost impossible to ascertain because the Trash Vortex is not a solid mass of materials, but rather a concentration of small plastic pieces on the surface of the water that penetrates as deep as 11 km or the entire depth of the ocean’s Pelagic Zone (any area in the ocean that is not close to the sea floor, or seashore). The Pacific Garbage Patch is not visible from space as a solid mass; making exact size measurements really difficult, because it is made up of high concentrations of small plastic pieces. Most of these pieces are microscopic to 1 square centimeter in size. The microscopic pieces are created by physical breakdown of larger pieces like plastic bags, or started out that size as micro abrasives in household and industrial cleaning products; so therefore, the only way of measuring the actual size of Trash Island is to take water samples at various points along the surface and at various depths. A further complicating factor is that there are no set parameters for how many parts per million (or other measures of concentration) that delineate the “island” from surrounding ocean, as there is some degree of pollution in the entire ocean. So what is the “cut off” line? One 2001 study found over 5000 grams of plastic per 1 square kilometer of ocean.

In addition to these plastics, on their own being harmful to the ocean ecology, they also absorb toxic chemicals such as bisphenol A and PCB’s, which get concentrated as they are consumed up the food chain. One example of their insidious danger is the zoo plankton. Fish and other marine animals eat the zooplankton (including krill) by filtering sea water. Plastic debris is mixed in , so any given mouthful of zooplankton will have a percentage of plastic pieces. Sea creatures are turning up dead, with accumulations of plastic in the stomachs, dying from malnutrition or poisoning. Mammals like whales who eat tonnes of krill daily, could be in real danger.

How Was Trash Island Formed?

Trash Island formed in the North Pacific Gyre. A gyre is a vortex of air or water. The North Pacific Gyre results from the Earth’s rotation causing a Coriolis Effect; a phenomenon whereby the Earth must, due to the laws of physics, rotate faster at the Equator, where the Earth’s circumference is the greatest, and not at all at the poles. An object, then moving north from the Equator will be deflected east, as the Earth turns slower moving away from the equator. Water and air move around the planet and are acted on by the Coriolis Effect, resulting in water vortexes, or places of debris accumulation; like how a tornado sucks in debris as it spins. Trash Island is then formed by garbage coming from the east coast of Asia; leaving the shore, it takes about 1 year or less to reach the North Pacific Gyre; and the west coast of North America; leaving the shore, trash takes about 6 years to reach the North Pacific Gyre.

How Can Trash Island Be Cleaned Up?

Boats, dragging large, fine gauge, nets filter out some of the garbage, but predictably, end up taking sea life with them. Project Kaisei: Capturing the Plastic Vortex is an initiative to study, clean up and create awareness about Trash Island and others like it around the Earth’s oceans. For more information, you can contact Project Kaisei.

Your entire digestive system.

Your stomach is located at the end of your esophagus and is the terminus for swallowed food and drink. The stomach receives chewed food and continues to mechanically and chemically break it down into smaller pieces, creating more surface area for your small intestine to absorb nutrients.

Your stomach is an acidic environment with a low pH of between 1 and 3. Parietal cells in the wall of the stomach secrete hydrochloric acid (HCl). If your esophageal sphincter; basically the lid to your stomach; isn’t closed properly, HCl will creep into your esophagus resulting in heartburn. HCl has a few different jobs. One, is to kill bacteria or other potentially dangerous pathogens you may have unknowingly ingested with your food. Another is to convert pepsinogen into pepsin. Pepsinogen is released from chief cells in your stomach wall. HCl, chemically changes pepsinogen into pepsin and is essential because pepsin doesn’t function in an environment with a pH greater than 5. Pepsin begins protein digestion by breaking it down into peptide chains. Peptide chains are made up of amino acids. Your small intestine absorbs amino acids into your circulatory system for distribution to the rest of your body. It is important to note there is a layer of mucus protecting your stomach from being chemically broken down by pepsin and HCl.

Parietal cells of stomach wall

Parietal cells in your stomach wall also secrete intrinsic factor; a substance whose only job – as far as scientists know – is to facilitate the absorption of  vitamin B-12.  Intrinsic factor cannot do its job in the acidic environment of your stomach; it works best in a pH of 7 – close to water – but is used later in your ileum to absorb vitamin B-12 into your circulatory system after bile from your gallbladder has neutralized the acidic chyme (what your partially digested food is called when it enters your small intestine). B-12 is vital for your red blood cells to carry oxygen. People who lack intrinsic factor, cannot absorb vitamin B-12 and suffer from pernicious anemia.

Chymosin, or rennin, is secreted by the chief cells in your stomach wall and is responsible for the breakdown of a specific peptide bond: phenylalanine and methionine, through a complicated chemical process that I won’t detail here. Interestingly, rennin is the active ingredient in rennet which is used the cheese production; compelling some vegetarians into eating cheese without rennet.

Gastric lipase (“lip” means fat and “ase” means breakdown) is secreted by the chief cells to begin fat digestion in your stomach by hydrolyzing (“hydro” means water and “lyzing” means breaking apart; so the breaking apart of a molecule using water) fat molecules into fatty acid chains. Further fat digestion happens in the small intestine with the addition of pancreatic lipase.

G-cells in the wall of your stomach secrete gastrin, a hormone responsible for stimulating the release of HCl from the parietal cells. Gastrin is a chemical messenger that travels in your bloodstream and is released when your stomach is distended from having recently eaten, or when directed to be released by your brain in response to the sight or smell of food. Gastrin stimulates the release of HCl and pepsinogen. It enhances the strength of your stomach contractions to aid in mechanical digestion and causes the pyloric sphincter to relax or contract, controlling movement of chyme that moves into duodenum, the first segment of the small intestine. Your duodenum can only process a certain amount of chyme at a time, so your pyloric sphincter opens and closes to allow small packets of chyme to enter at regular intervals.

In summary, your stomach breaks your food into smaller pieces and mixes it with all of the above secretions in mechanical digestion. Parietal cells secrete hydrochloric acid and intrinsic factor. Chief cells secrete pepsinogen, chymosin and gastric lipase. Mucus cells secrete mucus to protect the stomach wall from the acidic chyme. Gastrin is the hormone responsible for mobilizing the whole process.

The colon is the biggest part of the large intestine. Your entire intestinal tract between your stomach and your anus includes your small intestine that is divided into the duodenum, the jejunum and the ileum. Your large intestine is made up of your cecum, ( in anatomical order) the ascending, transverse, descending and sigmoid colon, rectum and anus.

The cecum is the small sac that connects to the ileum of the small intestine to the ascending colon. Chyme is the mostly digested food matter that enters the cecum from the small intestine. 90% of digestion has already taken place. The colon has no digestive enzymes, but positive intestinal bacteria called gut flora and mucus are added to the chyme to form feces. At this point, your body will reclaim water and vitamins; essentially concentrating the feces before it exits the body. Note; when you have watery poop, your colon is not reabsorbing water and vitamins from the feces; the last step in digestion is being skipped. This is one of the reasons why it is so important to stay hydrated when you have diarrhea.

One type of gut flora - Candida albicans

Now, a word about dietary fiber. We are constantly reminded to eat lots of fiber for colon health. But why? The bacteria in your large intestine consume the largely undigested fiber for their own sustenance, and give off acetate, propionate and butyrate as waste products which the cell lining of the large intestine uses as nutrients. It really is amazing how efficient our bodies are; the 3 R’s to the extreme.

What can go wrong?

Colitis (“col” is colon and “itis” means inflammation), not matter what the cause is a swelling of the large intestinal wall. It can caused by autoimmune processes, idiopathic (of unknown cause), vascular (an interruption of blood flow to a portion of the intestine), infectious (as is the case with clostridium difficile and e coli), or caused by parasites.

Hereditary or other causes of colorectal cancer affect approximately 7% of U.S. citizens.

Crohn’s disease is an autoimmune disorder where the body attacks the colon wall, causing colitis.

Major elements of the urinary system

The urinary bladder, as it is referred to anatomically to distinguish it from meaning “pouch or flexible enclosure”, sits atop your pelvic floor: protective layers of muscles and connective tissues designed to hold you internal organs in place. The bladder is the final internal destination for urine that has been collected and concentrated by the kidney and transported via the ureters – one for each kidney.

The urinary bladder; like the design of many other internal surfaces of your body, like the small intestine and the stomach is lined with folds of tissue. In the stomach and bladder, these folds are called rugae and they stretch and flatten in response to increased pressure – if you have just eaten a big meal or haven’t urinated in a long time. Our wonderful bodies follow this design because internal bladder expansion takes the pressure off the surrounding pelvic and abdominal organs. In contrast, if the bladder filled outwards like a balloon, our pelvic and abdominal muscles would be continually squashed.

We start feeling the urge to pee when our bladder is about 25% full. For most people; this pretty easy to ignore. Nerves on and near our bladder, when stretched, trigger the parasympathetic nervous system (the rest and digest part of our nervous system as opposed to the sympathetic fight or flight part of our nervous system) to signal us to go pee. As the bladder stretches, the PNS becomes more insistent that we go pee. If the bladder reaches 100% capacity you will expel urine involuntarily. The flow of urine is controlled by two muscles; an internal involuntary muscle called the detrusor muscle and an external voluntary Kegel muscle.

OK, a brief aside to explain involuntary and voluntary muscle: involuntary muscles are controlled directly by our nervous system without conscious input from us. They are made up of smooth muscle fibres. Skeletal muscle, under our voluntary control is also regulated by our nervous system, but we are the ones sending the signals to the brain to move or not move. Skeletal muscle is striated. Microscopically, they look very different from each other. Smooth muscles are working away in your body all the time; like for example, in your small intestine as the smooth muscles push food along the digestive tract towards the large intestine (or colon) and out the anus.

Kegel muscle a.k.a. the Pubococcygeus muscle

It is our voluntary muscle we contract to “hold pee in” You can strengthen this muscle by doing Kegel exercises – for women, flexing the little ring of muscles, inside your vaginal opening. Doing about 25 flexes of this muscle every day well help to prevent urinary incontinence problems when you are older. Men also have a Kegel muscle that allows their penis to stay erect, and controls their ejaculation and of course, help with incontinence. Men can isolate and strengthen this muscle by stopping and starting the flow when urinating. This is the same for women.

What can go wrong? Well it all boils down to incontinence, but for many different reasons. If you have damaged nerves, you may not be able to receive the PNS’s signals urging you to urinate as is the case with some Parkinson’s and Multiple Sclerosis patients. Your detrusor muscle (involuntary) is controlled by the PNS. If your PNS is damaged, this muscle may not function properly, and the only protection you have is your external muscle; which is likely not strong enough to hold back small outputs of urine. Prostate cancer can damage pelvic nerves resulting in incontinence.

Sometimes (mostly in women), if you laugh, sneeze or cough, the pressure it creates overcomes both sets of muscles resulting in little spurts of urine coming out. This is called Stress Incontinence and happens mostly in older women – over the age of 60, but can happen younger; say if you have a genetic predisposition to urinary incontinence.

Overactive bladder is diagnosed when you have to pee 8 or more times a day, and are up 1 or 2 times a night. Based on this definition approximately 1 in 6 people in the U.S. have this problem. OAB can be treated with antimuscarinic drugs or through a really cool sounding procedure whereby physicians insert an electrode near the tibial nerve in your leg. An electrical impulse travels to your sacral plexus via your tibial nerve. Recall, that your tibia is a bone in your lower leg. Your sacral plexus is a bundle of nerve fibers responsible for controlling parts of your pelvis and lower extremities. The treatment takes place once a week for 12 weeks. Some patients need more or ongoing treatment. I myself have an overactive bladder, but it doesn’t badly interfere with my life – excepting 11 hour long bus rides in Central Turkey with only one bathroom stop; I have just lived with it without treatment. Please understand, I am not a medical professional and I am not advocating any procedure or treatment, but just seek to educate people about our bodies and how they work. Peace out.