Biology 20 GATE

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SHR – Biology 20

                                      SHR – Smith & Huber Residence 
  This is a publication of the Smith & Huber Family members of the Smith & Huber Residence Copyright © Smith & Huber Residence 2007. All Rights Reserved This document is electronically protected to prevent editing or copying. Some portions and images of this document were taken from other sources. We do not credit all document content as our own. Care has been taken to trace ownership of copyright material contained in this text. The publishers will gladly accept any information that will enable them to rectify any reference or credit in subsequent printings. The information and activities in this textbook have been carefully developed and reviewed by professionals to ensure safety and accuracy. However, the publisher shall not be liable for any damages resulting, in whole or in part, from the reader’s use of the material. Although appropriate safety procedures are discussed and highlighted throughout the textbook, the safety of students remains the responsibility of the classroom teacher, the principal, and the school board district. Instruction on Concepts, Problems and Applications 2

CONTENTS: PREFACE TO BIOLOGY 20............................................................................................. 6 THE CELL MEMBRANE................................................................................................ 7 Passive Transport ........................................................................................................ 8 Active Transport ......................................................................................................... 9 DIGESTION AND HUMAN HEALTH .......................................................................... 10 MACROMOLECULES AND LIFE ............................................................................... 10 Carbohydrates ........................................................................................................... 10 Lipids ........................................................................................................................ 11 Proteins ..................................................................................................................... 11 Nucleic Acids............................................................................................................ 12 Vitamins and Minerals.............................................................................................. 12 Enzymes.................................................................................................................... 13 DIGESTIVE SYSTEM ANATOMY ................................................................................ 14 The Three Categories of Digestion ........................................................................... 14 Physical Digestion .................................................................................................... 14 Chemical Digestion – The Stomach ......................................................................... 15 Chemical Digestion and Absorption – The Small Intestine...................................... 16 Excretion – The Large Intestine................................................................................ 20 THE HUMAN CIRCULATORY SYSTEM .................................................................... 21 THE HEART.................................................................................................................. 21 Blood Vessels............................................................................................................ 22 Pace of the Circulatory System Via Heartbeat ......................................................... 23 Blood Pressure .......................................................................................................... 23 Cardiac Output .......................................................................................................... 23 Pathways Of The Circulatory System....................................................................... 23 BLOOD ......................................................................................................................... 25 Red Blood Cells ........................................................................................................ 25 White Blood Cells..................................................................................................... 25 Platelets ..................................................................................................................... 26 Blood’s Functions ..................................................................................................... 26 Circulation & Capillaries .......................................................................................... 27 Blood Disorders ........................................................................................................ 27 THE LYMPHATIC SYSTEM ......................................................................................... 28 3 SHR – Biology 20

Lymphatic Defense System ...................................................................................... 28 Blood Types .............................................................................................................. 30 Immune System Disorders........................................................................................ 31 THE HUMAN RESPIRATORY SYSTEM...................................................................... 32 STRUCTURE OF THE RESPIRATORY SYSTEM........................................................ 32 BREATHING AND RESPIRATION .............................................................................. 34 The Mechanics of Breathing..................................................................................... 34 Respiratory Volume .................................................................................................. 34 Gas Exchange and External Respiration................................................................... 35 RESPIRATORY HEALTH ............................................................................................. 35 CELLULAR RESPIRATION........................................................................................... 37 AEROBIC CELLULAR RESPIRATION STEPS............................................................ 37 Oxygen’s Importance................................................................................................ 39 ANAEROBIC RESPIRATION ....................................................................................... 40 FERMENTATION ......................................................................................................... 40 Lactic Fermentation .................................................................................................. 40 Ethanol Fermentation................................................................................................ 40 PHOTOSYNTHESIS........................................................................................................ 41 The Light Dependent Reactions of Photosynthesis ...................................................... 41 ....................................................................................................................................... 42 The Light Independent Reactions of Photosynthesis.................................................... 43 MUSCLE CONTROL ...................................................................................................... 44 SKELETAL MUSCLE ................................................................................................... 45 Skeletal Muscle Cooperation .................................................................................... 45 Skeletal Muscle Fibers.............................................................................................. 45 How Muscle Fibers Contract .................................................................................... 46 Creation of Energy Required for Muscle Contraction.............................................. 48 MUSCLES AND HEALTH............................................................................................ 48 Common Ailments of Muscles ................................................................................. 49 Muscle Twitch .......................................................................................................... 49 Slow Twitch and Fast Twitch ................................................................................... 49 THE EXCRETORY SYSTEM ......................................................................................... 50 ANATOMY OF THE EXCRETORY SYSTEM ............................................................... 50

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The Kidney................................................................................................................ 50 URINE PRODUCTION ................................................................................................ 52 Proximinal Tubule .................................................................................................... 52 Loop of Henle ........................................................................................................... 52 Distill Tubule ............................................................................................................ 53 Collecting Duct ......................................................................................................... 53 Summary ................................................................................................................... 54 MAINTAINING THE EXCRETORY SYSTEM .............................................................. 55 Salt Reabsorption ...................................................................................................... 55 Maintaining Blood pH .............................................................................................. 55 Renal Insufficiency ................................................................................................... 56 Dialysis ..................................................................................................................... 56 ENERGY TRANSFER IN THE BIOSPHERE ................................................................ 57 ENERGY ENTERS THE BIOSPHERE ......................................................................... 57 The Sun Provides Energy.......................................................................................... 57 Life Under The Sea................................................................................................... 58 Consumers................................................................................................................. 58 Energy in the Biosphere............................................................................................ 59 ENERGY TRANSFER WITHIN THE BIOSPHERE...................................................... 59 Ecosystems Within the Biosphere ............................................................................ 59 Food Chains and Webs ............................................................................................. 60 Biomass Pyramids..................................................................................................... 61 CYCLES OF MATTER.................................................................................................... 62 THE HYDROLOGICAL CYCLE................................................................................... 62 Water at the Chemical Level..................................................................................... 62 Water Within the Ecosystem and Biosphere ............................................................ 63 Uses of Water............................................................................................................ 64 BIOGEOCHEMICAL CYCLES .................................................................................... 65 The Carbon and Oxygen Cycles ............................................................................... 65 The Sulfur Cycle ....................................................................................................... 66 The Nitrogen Cycle................................................................................................... 66 The Phosphorous Cycle ............................................................................................ 67 Final Notes ................................................................................................................ 67

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PREFACE TO BIOLOGY 20 The cell is the smallest unit of life known in living creatures. In order to gain an appreciation and understanding for modern day Biology, we need to first understand the structure and functions of the microcellular components, and how the cells interact. Both plants and animals, as well as some bacteria and fungi, are made of eukaryotic cells, or cells with a nucleus. Although the plant cell has some organelles specific to only itself, the animal cell organelles are the same for any cell. Below is a diagram of a animal cell, and its components:

The cell membrane is a structure on the outside of the cell that acts as a semi-permeable barrier between the outside world and the inside of the cell. It also controls the transport of particles into and out of the cell. All the organelles of the cell live in a gel like substance cytoplasm which is comprised of the chemicals required to sustain life, and minerals that can be absorbed for energy. Alike a City Hall, the nucleus is the command center of the cell. It contains the imprinting of DNA in order to create the proteins responsible for cellular functions, the basic components of life. It is surrounded by a double layer of membrane to protect it from radioactivity. The chromatin is the unchained DNA strands within the nucleus. The nucleus requires the ability to take in macromolecules and send ribosome out. Nuclear pores serve that function. Ribosome help to build proteins and are comprised of two tiny structures working together. Instruction on Concepts, Problems and Applications 6

Endoplasmic Reticulam (ER) are thin tubes and sacs of membrane that extend from the nucleus outwards. Rough ER synthesizes proteins due to the fact that it is studded with ribosome and smooth ER with transports macromolecules to other points in the cell. The Golgi Apparatus receives the macromolecules from the smooth ER, and package them into vesicles, using proteins and lipids and prepares them for secretion out of the cell via the cell membrane. A very important organelle, the mitochondrion receives carbohydrates and other particles of food, and converts it into useable energy which is released for the cell. In contrast, the lysosome breaks down old and damaged or expended cell parts. The peroxisome also acts as a digester, handling toxic waste products, such as alchohal. The centrosome ensures the even distribution of cell organelles in the event of cell duplication. Its dual centrioles and close proximity to the nucleus help facilitate this. There are two different types of transport “containers” within the cell, varying on the size. Vesicles are small sacs that move small amounts of particles inside or outside of the cell. The vacuole is a massive fluid filled sac that serves as a storage facility for food, sugar energy and waste. The cytoslekeleton ensures that the cell retains a useable shape, through a system of three fibers, actin filament, micro filament and microtubules. THE CELL MEMBRANE The Cell membrane serves a key purpose, it acts as a guard against contaminated particles, and as a receiver for energy and food for each cell. Usually, the cell membrane is two layers thick, with the inside being comprised of lipids (fat particles that are not dissolvable in water). The lipids have a sperm-like design, with a head and a tail. The head dissolves easily and readily in water, while the tail is insoluble. Primarily, the tails are touching inwards in the cell membrane, so that the outside of the membrane is porous to water, and the inside can be semi-permeable.

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Other particles in the cell membrane facilitate transport of macromolecules into the cell, and create passageways for water to flow. Particles and ions can cross the membrane of the cell in a variety of ways. These methods can be either classified as passive, where heat energy is used to move the particles, or active; where both heat and energy from sugars are used. Passive Transport Passive transport refers to molecules moving from areas of greater concentration to areas of lesser concentration. This is also known as movement with the concentration gradient. All methods of passive transport move with the concentration gradient, and therefore do not require energy from sugars. One method of passive transport, diffusion, works on the natural principal of particles and ions to move naturally from areas of greater concentration to areas of lesser concentration, across the semi-permeable cell membrane (imagine dumping food coloring into water, such as the figure right). Many molecules, such as oxygen are able to move via diffusion, and cannot be readily stopped by the cell membrane, due to its permeability. The diffusion of a solvent, such as water is known with a special term, osmosis. Which direction osmosis occurs depends once again on the concentration gradient. If there is an equal concentration of solvent particles inside and outside of the cell, (isotonic) there is no osmosis occurring. If the cell is hypertonic, that means that there is more water inside the cell then outside, and water flows freely out of the cell. Likewise, if the cell is hypotonic, water flows in, as there is less water inside the cell then outside. Facilitated diffusion permits molecules that are too large to simply diffuse through the membrane into the cell. Glucose molecules enter the cell through utilizing special carrier proteins (see figure left), which facilitate the diffusion. The carrier proteins will only accept a non-charged molecule with a certain shape. Charged ions pass through tunnels, known as channel proteins, which will only fit certain sized ions, in order to help them diffuse into the cell (see figure right).

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Active Transport Active transport requires one of the photospheres in ATP (adenosine Triphosphate) sugar created for the cells be split in order to release energy, which can then be applied to actively transporting materials the opposite direction from the concentration gradient. The cell membrane can fold, and create vesicles to take in particles which usually would not fit inside of it. The process where the cell membrane folds in order to take in a molecule (such as cholesterol) is known as endocytosis. Endocytosis has three forms, pinocytosis, phagocytosis and receptor assisted endocytosis. Pinocytosis refers to the movement of small liquid particles, whereas phagocytosis is the movement of larger droplets of intercellular fluid, bacteria or organic matter. Receptor assisted endocytosis involves using a special membrane receptor protein that will latch onto the molecule it is made for and transport it into the cell. All three methods of endocytosis are shown in the figure right. Exocytosis removes cell wastes from the cell by having a vesicle transport the waste to the cell membrane, and then latching onto the membrane, and opening to release the waste into the fluidic space between the cells.

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DIGESTION AND HUMAN HEALTH Within the body lies the cells. In between the cells is fluid and blood. And within that fluid are thousands of different particles. Some, such as water and oxygen, are simple enough. Other large complicated collections of molecules, known as macromolecules are grouped into four categories: carbohydrates, lipids (such as fats), proteins, and nucleic acids. Many macromolecules form polymers, long chain of repeating chemicals that control the most important functions of the body. MACROMOLECULES AND LIFE Macromolecules are assembled in much the same way. Chains are created by removing a –OH group from one subunit of the chain, and an H atom from the other subunit on the chain. This results in a loss of a water molecule, H2O. Hence, this reaction is called dehydration. Disassembly is a direct opposite, a –OH molecule is added to one subunit and a H atom is added to the other, breaking down the link. Disassembly is called hydrolysis which is Greek for “water” and “break”. The process of creating and destroying these bonds is carried out by a special class of proteins called enzymes, spoken about later on in this section. Carbohydrates Carbohydrates are macromolecules that contain carbon, hydrogen and oxygen and usually in the same proportions (two hydrogen atoms and one oxygen atom for each atom of carbon). Carbohydrates provide short or long term energy storage for a creature. There are two main types of carbohydrates. Simple sugars are made up of three to seven carbon atoms, and the corresponding number of hydrogen and oxygen atoms. On their own, simple sugars are known as monosaccharides while in pairs they are called disaccharides. Simple sugars are synthesized and desynthesized according to the process noted above, and shown in the figure left. The disaccharide, maltose, is commonly found in alcoholic beverages.

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Carbohydrates that carry more then two simple sugars are known as polysaccharides. Some common examples of polysaccharides are starch, which performs an energy storage function in plants, glycogen, which performs the same function in animals. Plants also have access to a third polysaccharide, cellulose, which is found in their cell walls. Highly rich in nutrients, cellulose only has a few organisms known to possess the ability to break the down. Herbivores such as rabbits must host theses organisms in order to harvest the energy from cellulose, while humans (who do not host these organisms) cannot access this energy. All three of the above polysaccharides, glycogen, starch and cellulose are shown in structure on the right. How are they different? Lipids Lipids are a group of macronutrients that are not soluble in water. They have many functions, including forming cell membranes, storing energy and fat (they store 2.25 times more energy then carbohydrates) or forming steroids, which are sex hormones estrogen and testosterone. Lipids exist in our food as fats, such as those in solid or liquid form. Fats are solid at room temperature, and are found in butter and many other dairy products (among other things), while oils are liquid at room temperature, and are found in salad dressing and other liquids. The formation of fats is actually quite interesting. The glycol molecule reacts with three fatty acids to form a triglyceride (see figure left). Triglycerides are composed similarly, however the fatty acids may be difference in size or in saturation. Saturated fats are triglycerides where the fatty acids does not have a covalent bond between its carbon atoms, which means that it contains all the hydrogen ions that it could possibly bond with. Unsaturated fats do have double bonds between the hydrogen atoms. Saturated fats are usually solid at room temperature, while unsaturated fats are usually liquid. Next time you purchase a food product from the store, see if you can spot the saturated fats content on the label! Proteins Proteins are a highly unique component of the macromolecule family, due to the vast variety of configurations that can exist. Proteins exist in your cells, coordinating

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operations, control your muscles, make up your hair and fingernails and connect your bones. The reason that they can have such diversity has to do with their composition. Like other macromolecules, proteins are assembled into subunits. These subunits are known as amino acids and are comprised of a central carbon atom bonded to a hydrogen atom and three other -COOH) and groups of atoms, an amino group (-NH2), an acid group (carboxyl an R group. The R group is one of twenty-three different potential items that distinguish the amino acid from another. The human body can only synthesize 11 of the 23 groups. The others must come into the human body from your diet, and are thus termed essential amino acids. Amino acids join together forming peptide bonds in order to become proteins. A peptide bond is alike the one shown in the figure, above. In dehydration synthesis, two amino acids form a bond called a dipeptide. The R group does not participate in the bonding. The different amino acids of the chain repel and attract each other, forming a coil, such as the one in the computer generated picture to the right. This gives the protein specific functionality and a three dimensional structure. The protein’s solubility in water is also determined by its R group. Water soluble R groupings, such as those within enzymes and hemoglobin, are on the outside of the chain and are usually electrically charged. Non-water soluble R groupings, with no charge, alike the proteins in your fingernails, are coiled on the inside of the protein. Nucleic Acids Nucleic acids are the building blocks of life. Their configurations and subunits determine the order and production of the proteins that run all bodily functions. RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) are two kinds of nucleic acids. DNA contains genes, and copies over the genes to RNA to produce proteins. Nucleotides are the different subunits that DNA and RNA are made up of, and only four are known to exist. Vitamins and Minerals Vitamins and Minerals are key components of many cell reactions, and are usually utilized as a important tool to run cellular operations. Specifically, vitamins are organic compounds, of which very little are needed for the body. They are coenzymes, which help with the production of the enzymes. Vitamins also assist in keeping our skin tissue

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intact. Minerals are non-organic compounds, which assist with many chemical reactions such as building bones and cartilage, and are components of hemoglobin, hormones and enzymes. Enzymes Lastly on our brief biological chemistry tour, are enzymes. Enzymes act as catalysts in chemical reactions, speeding them up thousands of times then their usual pace if performed in a laboratory. While temperature can increase the speed of reactions in the body (for example, the reason you get a temperature when you have the flu, is because the body is trying to speed up all the biochemical reactions and eliminate the infection quicker), it can also cause proteins to become denatured, or in other words lose their three dimensional shape. So, how do enzymes speed reaction times? Well, enzymes are made like puzzle pieces, so that they fit perfectly with the specific substrate, or molecule that the reaction time is being increased. By fitting perfectly, the bonds on the substrate become weaker, and are more easily broken, and more ready to react. Enzymes have a limited life span, and must be synthesized by cells on occasion. Enzymes can be inhibited by changes in temperature or pH. When the temperature becomes too low, enzyme bonds become too brittle to fit the substrates. When the temperature becomes too high, the bonds are too weak to work well with the substrates. Similarly with pH, enzymes usually work best between 6 and 8 on the pH scale (although some enzymes work much better under much more acidic conditions, like stomach enzymes). Inhibitors can also hinder substrates and enzymes from connecting, by blocking the path to the enzyme’s active site. Competitive inhibitors attach directly to the active site, and compete for the enzyme with the substrate. Non-competitive inhibitors attach elsewhere on the enzyme and alter its shape and chemical structure, making it far less effective because it no longer perfectly fits the substrate.

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DIGESTIVE SYSTEM ANATOMY Multicellular organisms, like mammals and more specifically: humans cannot simply have their cells collect food and use it for cellular operations. Instead, we use our digestive system to take in food, and digest the useful components of the food, breaking them down into nutrients that can be transported to our cells via the blood stream, and then utilized for cellular operations. This gigantic and daily task is worked on by our own digestive system. Some of the key organs in our digestive system are shown on the right. Imagine simply how large this system is. There are 8 meters worth of tubing from your esophagus to your anus. And food and nutrients pass down this trail every single day. We’re going to learn about the process the food follows in this section. The Three Categories of Digestion Digestion occurs in three distinct ways: 1. Physical Digestion which is where the food is broken up into pieces physically. This usually occurs in your mouth, with your teeth. 2. Chemical Digestion which is where chemicals break the food down into its key components. Your saliva, your stomach and your intestines take care of this. 3. Excretion is the removal of the excess from your body, either via solid or fluid. Physical Digestion Physical digestion begins immediately when you take food in. Your teeth begin to chew the food, as your tongue moves the food around your mouth. Saliva moistens the food, and amylase from the saliva helps to break the chemical bonds in food to make it easier to chew. Eventually, the tongue and teeth make the food into a squishy lumpy substance called bolus which your tongue pushes to the back of your throat. At the back of your throat there are two tubes, one is the trachea, which connects to your lungs. The other is the esophagus, where your food is swallowed and travels down to

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your stomach. To prevent food from escaping down your trachea, the epiglottis, a small piece of cartilage, and the trachea jut together, sealing off your windpipe when you swallow. Your “Adam’s apple” can be felt as it pushes upwards when you swallow, sealing your windpipe. Secretion Saliva Mucus Site of Production Mouth Mouth, stomach, small intestine, and large intestine Mouth, stomach, small intestine and pancreas Stomach Liver (stored in gall bladder) Function Contribute to digesting starch, by the creation of amylase. Lubricates food to help with swallowing. Protects the cells lining the digestive tract from erosion by acidic chemicals, lubricates Assists in digestion of molecule so that they can be broken down into nutrients that can be absorbed into the blood stream. Promotes digestion of protein Suspends fats in water using basic salts and cholesterol, to assist in emulsification in the small intestine. Neutralizes stomach acid when it reaches the small intestine. Stimulate the production of bile, acid, enzymes and bicarbonate and their release in order to help oversee peristalsis.

Enzymes Acid Bile

Sodium Pancreas and bicarbonate small intestine Hormones Stomach, small intestine and pancreas

Your esophagus moves the bolus from your mouth to the esophageal sphincter (a circular muscle that acts as a valve, opening to admit bolus into the stomach, but remaining shut so that the acid in your stomach does not escape up into your throat) partially via gravity and partially via routine contractions in the esophagus’s longitudinal muscle. The diagram to the right shows this. Chemical Digestion – The Stomach The bolus has now passed through the esophageal sphincter entered the stomach. Your stomach is alike an accordion, comprised of many folds of muscle that can unfurl and expand when the demand is needed.

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At its smallest point, the stomach is able to hold about 50 mL of food. After it expands, it can hold 2-4 L of food. Amazing! The stomach is an enclosed system, with a true sphincter muscle, known as the pyloric sphincter located at the bottom, leading to the entrance to the small intestine. Inside the stomach, the bolus is tossed around, via contractions and expansions about the smooth muscle folds in the stomach, and mixed with gastric juices in order to assist in digestion. Your stomach produces 2-3 L of gastric juices a day. Primarily, these juices are comprised of hydrochloric acid, enzymes, mucus, salts and water. The pH of this substance varies between 1 and 3, making the stomach highly acidic. The pH is part of the reason the stomach has the sphincter muscles at either end; so that acid cannot escape and begin to erode the small intestine. Acid does escape into your esophagus, as the esophageal sphincter is not a real sphincter; causing it to feel raw (this is commonly known as heartburn). This is the function that also allows you to vomit. Your stomach has three levels of production to ensure that its acidity does not erode the stomach walls. First, the hormones that cause the secretion of gastric juices do not activate very much until food is present. Secondly, the mucus secreted by the stomach protects the muscle walls from being attacked by the acid. Thirdly, the stomach’s enzyme for digestion – pepsin remains inactive until the presence of hydrochloric acid is detected, only then does it create polypeptides which begin to digest protein prior to the entrance into the small intestine.

Chemical Digestion and Absorption – The Small Intestine The small intestine, although small in diameter, is four times the length of the large intestine. It is primarily responsible for the digestion of food and its absorption into the blood stream. Segmentation of the small intestine occurs via the contractions of the muscles in the intestine, sloshing

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the chyme back and forth through the intestine, while still feeling the pull of peristalsis. Overall, the small intestine can be divided into three regions. The first, the duodenum is approximately 25 cm long. Ducts from the liver and the pancreas both enter into the small intestine at this point. The walls of the small intestine are covered with small villi, finger like projections. On the villi are tiny hairs known as microvilli. Each of these structures is directly connected to the circulatory system, and they are responsible for moving useful nutrients from the intestine into the bloodstream. The second and third regions of the small intestine, the jejunum and the ileum respectively, have similar functions to the duodenum. The 2.5m jejunum contains additional folds and more secretion glands the duodenum. The ileum, which is 3m long contains less villi and glands, and is mainly designed to absorb the last of the available nutrients, and push the chyme into the large intestine. Supplementary Organs The small intestine has a large variety of supplementary organs that assist in digestion including the pancreas, liver and gal bladder. The pancreas delivers approximately 1 L of pancreatic fluid to the duodenum daily. Pancreatic fluid includes: trypsin and chemotrypsin, which digest protein, pancreatic amylase which digests starch not already handled by the salivary amylase and lipase, which digests fat. The enzymes released from the pancreas are not activated immediately, not until a certain enzyme is released from the hairs on the duodenum. Proteins are then digested into smaller polypeptides, polysaccharides into simple sugars and fats into fatty acids and other products. Pancreatic fluid also contains sodium bicarbonate, which neutralizes the chyme from the stomach, returning it to a stable pH of 8, which helps to increase the effectiveness of the other enzymes in the small intestine. The liver is the largest organ in the adult body. One of its many purposes in the body is to produce bile, the byproduct of destroyed red blood cells. Although the components of the cells (known as bile pigment) are useless and are eventually excreted from the body, the salts that is also produced in bile are hugely useful as an emulsifier – a chemical that

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breaks down fat molecules into smaller molecules so that they can be more easily absorbed into the blood stream. The liver does not store the bile between meals. Instead, the gall bladder, which is connected to the same duct as the liver, stores the bile and secretes it upon activation from the duodenum hairs. Digestion & Absorption Digestion occurs, depending on the type of nutrient, by a different enzyme. Carbohydrases dissolve carbohydrates, lipases dissolve fats, proteases dissolve larger polypeptides and nucleases dissolve other nucleic acids. The below image and table show you the different macromolecules being digested, and how they are digested.

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Specific Digestion by Nutrient Carbohydrates and starch are digested via amylase. This digestion starts in the mouth, with the salivary amylase. Amylase works best at a pH of eight (about neutral) so the harsh acidity of the stomach results in the digestion of starch ceasing. When the chyme enters the small intestine (pH of about 8), the amylase can again begin its work. Pancreatic amylase, which is secreted into the small intestine, also assists in digestion. Starch is reduced to disaccharides and then are further broken down by other carbohydrates into glucose, galactose and fructose (monosaccharide). These monosaccharides are then absorbed via active transport into the villi, who transfer it to the liver, which converts the sugar to glucose and circulates it throughout the bloodstream. Protein is digested mostly in the stomach, by the polypeptides secreted via pepsin. The peptide and the undigested protein enter into the small intestine, where trypsin and chymotripsin are both secreted, hydrolyzing the polypeptide bonds and forming small chains of peptide. The protein is fully digested, and another enzyme secreted by the pancreas breaks the peptide back down to its core elements and are then absorbed into the bloodstream for processing by the liver. The liver determines the function of the pepsin, either utilizing it in energy releasing reactions to create sugar, or distributing it to the cells to perform a wide variety of functions. Fat is first emulsified in the small intestine by the lipases. This reaction is physical, not chemical, although the fat is split up, it still remains the same chemical composition and can now simply diffuse across the villi. Once inside, fat is coated with proteins and

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is reorganized back into triglycerides and are transported into the chest area by the lymphatic vessels. The protein is then stripped, and the fat goes back into the bloodstream to be circulated around the body. Nucleic acids are digested in a very similar fashion, with nucleodiases breaking them down into their bases, sugars and phosphates, which are moved into the bloodstream via active transport. Excretion – The Large Intestine The large intestine is much smaller in length then the small intestine (confusing, I know). It is only 1.5 m long and its primary function is to ready all the leftover chyme that was not digested for excretion. On an average day, the large intestine takes 500 mL of unused material and squishes it down to a 150 mL waste product. The undigested chyme passes through the colon, which removes any water that remains in the chyme so that the body does not become dehydrated while anaerobic bacteria break down the last nutrients in the chyme, usually generating Vitamin K and Vitamin B-12. The feces that are generated from the leftover chymen, and pass into the rectum – the last 20 cm of the large intestine. The rectum has three folds, one which allows it to pass gas, another which you control when you want the rectum to empty, and the third which allows the feces to exit the body by peristalsis, when full.

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THE HUMAN CIRCULATORY SYSTEM Multicellular organisms require a complex structure of specialized cells carrying out specific functions in order to maintain day to day operations. In humans, this is taken care of by the circulatory system. Primarily, the circulatory system has three functions: 1. Transport of gasses (from the respiratory system), nutrients (from the digestive system) and wastes (from the excretory system) 2. Regulates the production of hormones to stimulate certain cells in the body; causing key operations within the body, and controlling temperature and pH level. 3. Protection against blood loss, and against toxins entering the body system. THE HEART The heart is a key component of the circulatory system, ensuring the flow of blood throughout the body, and also facilitating the reoxidization of blood from the respiratory system. It also ensures that blood can only travel in one direction by putting an immense amount of pressure on the blood, over a lifetime enough pressure is exerted to lift a battleship through the water. Approximately the size of two fists, the human heart is located just of to the left in the chest. It contains four chambers, two atria (singular: atrium), on the top, which take in oxidized blood from the lungs and deoxidized blood from elsewhere in the body, and the ventricles in the lower portion of the heart, that take the blood from the atria and pump it to the lungs or to the body. The heart is made of strong cardiac muscle that involuntarily contracts rhythmically for the duration of a life. You cannot consciously cease or alter your heart beat. In between the left and right atrium is a thick muscle wall called the septum. The right atrium of the heart receives deoxidized blood from the body. The Superior Vena Cava receives deoxidized blood from the lungs, chest and head area. The Inferior Vena Cava collects blood from the lower portions of the body. All the collected blood flows downward into the right ventricle before passing into the pulmonary trunk, and then into the pulmonary arteries for transport to the lungs. The Pulmonary Veins on the left side of the heart take the oxidized blood from the lungs, and pass it through the atrium. After passing through the left ventricle, the blood is pumped up through the largest blood vein in the body – the aorta.

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The heart is made up of four different valves, as shown on the right. The atrium and ventricle are separated by the atrioventricular valves, the bicuspid (left side) and the tricuspid (right side. The other valves, the pulmonary and aortic semilunar valves permit blood flow from either the body (deoxidized blood) or the lungs (oxidized blood). Blood Vessels The body contains three major blood vessels, one is the arteries (which carries oxygen rich blood to the other parts of the body away from the heart). Veins carry oxygen deprived blood back to the heart for reoxidization. Capillaries are the small blood vessels that connect the arteries and veins, and where nutrients, minerals and wastes are transferred into the bloodstream. • As shown in the diagram on the right, arteries are stretchy and expandable. This is especially useful when the heart sends a large jolt of blood up against gravity (for example to the head region). Veins are not elastic, but are brittle and cannot be expanded. However, veins do have one way valves, to prevent blood from flowing backwards. Capillaries transfer blood from the arteries to the veins. Capillaries are very small, about ten stacked side by side (width wise) would have the diameter of a human hair. They are small enough that only one red blood cell can pass through them at a time, which helps to ensure that nutrients and other materials

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for the respiratory system are carried efficiently in the blood. Pace of the Circulatory System Via Heartbeat The SA Node, which is a clump of nerve endings located on the right atrium of the heart, is referred to as the pacemaker of the heart, as its stimuli forces the heart muscle to contract and relax rhythmically. The electric signal from the SA node results in the two aorta contracting almost simultaneously. The signal next spreads down the heart to the atrioventricular node which spreads the connection out to conductive Purkinje fibers, which initiate the simultaneous contractions of the ventricles. Blood Pressure When the heart beats, more blood flows into the arteries, pushing up against the artery walls and the muscles. When the ventricles in the heart contract to the maximum, it is called systolic pressure. The lowest pressure is the diastolic pressure. Blood pressure is measured in mmHg, or millimeters of mercury, which can be converted to kilopascals upon desire. Blood pressure is measured as systolic pressure divided by diastolic pressure, represented in a fraction. Cardiac Output Cardiac output refers to the overall ability of the heart to supply blood and oxygen to the muscles, permitting the body to do work. It is usually in the units mL/mm (milliners per millimeter). Cardiac output is calculated based upon the following formula: Cardiac Output = Heart Rate Stroke Volume

Heart Rate is the number of times your heart beats per minute, while Stroke Volume is the amount of blood that is pushed with each beat. Stroke volume is based upon the amount of blood that enters the atrium, and the strength of the ventricular contractions. Pathways Of The Circulatory System The circulatory system moves the blood throughout the body. There are three different pathways the blood may follow, the pulmonary pathway, which delivers blood that is oxygen poor to the lungs where it is released of its carbon dioxide and given new oxygen, via the respiratory system. The systemic pathway moves oxygen rich blood from the left ventricle of the heart into the body tissue for utilization and waste disposal. The coronary pathway is solely

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dedicated to keeping the heart equipped with blood. The diagram on the left helps depict these paths. The below cycle chart shows an abbreviated version of oxygen movement in the body, that you’ve learned about thus far:

Blood travels through the veins back to

Oxygen poor blood returns to heart from

Flows through vena cava to right atrium Heart contracts, and blood is pumped into the right ventricle.

Blood delivers payload of oxygen, and receives waste.

Heart contracts, and blood is pumped into the pulmonary arteries

Blood is transferred throughout the body via the arteries

Pulmonary arteries lead to lungs

Heart contracts, blood is pumped into systemic system. Heart contracts, blood enters left ventricle

Gas exchange takes place in the capillaries, oxidizing blood

Heart contracts, blood enters left atrium

Blood continues into pulmonary veins

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BLOOD Blood is considered to be one of the major connecting apparatuses in the body. It carries oxygen to the muscles and cells, and removes their carbon dioxide. It transports these materials back and forth and participates in gas exchange in the lungs. But this is not the only function of the blood. Blood is fluidic, or at least fluidic in appearance. It contains both a fluid and a solid portion. The fluid is the plasma of the blood, which contains water, dissolved gasses, hormones, vitamins and minerals. The solid blood or the formed portion consists of the white and red blood cells and platelets . The formed portion of the blood is produced in the bone marrow. The tube on the right shows the percentages that each part of the blood makes up of the whole.

Red Blood Cells Red Blood Cells or erythrocytes, carry oxygen throughout the body. The amount of oxygen that can be moved depends on the quantity of the red blood cells, and the amount of hemoglobin they contain. Hemoglobin, a respiratory pigment, has special properties that allow it to pick up and transport oxygen, then release it via diffusion to the cells that need it. There are more then 280 million hemoglobin cells in each red blood cell. Hemoglobin also assists in the transport of waste materials. When carbon dioxide enters the blood a portion of it is picked up by the hemoglobin. Anemia is the condition where there is a lack of red blood cells in the body either for the reason that there is not enough iron intake in the diet, or due to another reason. People with anemia, may suffer from fatigue, and have pale skin. White Blood Cells

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White blood cells or Leucocytes are comprised of three main items granulocytes, monocytes, and lymphocytes. Granulocytes consist of neutrophils, basophils, and eosinophils, each of which is specialized. Monocytes leave the bloodstream and attack certain bacteria. Granulocytes, like monocytes engulf and destroy foreign bodies within the blood stream. Lymphocytes serve as antibodies who incapacitate pathogens. Platelets Platelets facilitate blood clotting, which prevents excessive blood loss in the event of a breach into the blood vessels. The process for clotting to occur is as follows: 1. Blood rushes to the area of injury. 2. Platelets release series of chemicals to form enzyme thromboplastin. 3. In the prescience of calcium, a reaction with prothrombin creates thrombin. 4. Thrombin reacts with fibrinogen (another plasma protein) to produce fibrin. Fibrin makes an insoluble material that is insoluble. This is the “scab” of your wound. Blood’s Functions Blood has many functions. One of the functions, as we’ve learned, is transport. Blood transports nutrients absorbed in the capillaries of the digestive tract, as well as nutrients that are synthesized in other areas. Blood also takes gasses from the respiratory system. Blood also works to transport waste materials from the cells, such as uric acid and carbon dioxide. The bloodstream also transports hormones, chemical messages that instruct the body to do certain things. Blood and the Regulation of Temperature Blood also plays an important role in the regulation of temperature in the body. Blood from the internal body passes through the skin in order to lose heat. When the body environment is too warm, blood pumps from the insides of the body out to the external skin portions of the body, which are cooler and help the blood to lose heat. The arteries nearest to the edge of the skin dilate in a process known as vasodilatation (see figure on the right). Sweating, and other mechanisms help the skin to lose the excess heat. Vasoconstriction is the outer blood veins constricting in order to conserve body heat when the body is cold. This usually leads to waves of muscle contractions, or shivering. Several factors lead to vasodilatation or vasoconstriction, such as blood pressure. The brain is able to regulate blood pressure by dilating or constricting the outer blood veins. Metabolic activity, and exercise can also lead to vasodilatation Countercurrent is the principal that makes this system of regulation possible. As warmer blood flows from the core of the body, it flows along a deep artery, that runs deep inside

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the body, not near the surface of the skin. This ensures that heat is kept to the extreme dies. Once the capillaries transfer the blood into the veins, the blood can either flow via the deep or surface veins, depending on the temperature regulation. Circulation & Capillaries Capillaries are very important to blood circulation because they provide the only apparatus where exchange of materials in blood can take place. Capillaries exist near most cells and in high concentrations in the lungs to facilitate the exchange of materials. A bed of capillaries lies between a artery and a vein, as per the image on the left. Not always are all the capillaries open. Sometimes, if necessary, the blood can bypass the capillaries and flow directly from artery to vein, through the opening and closing of tiny sphincter muscles. Exchange of materials in the capillaries takes place through the interstitial fluid. Within the capillaries, exchange of materials takes place via the concentration gradient. For example, if the blood is deoxidized, the concentration gradient will automatically result in the diffusion of oxygen into the blood stream. The need of hemoglobin to have oxygen also contributes to this movement. It also works the same way with the giving of waste products. Blood pressure becomes lower then that of the arteries in the capillary beds, and is lower yet still in the veins, in order to facilitate blood flowing through the capillaries, which it does at a slower rate of speed then its speed through the veins.

Blood Disorders

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Some major diseases of the blood include hemophilia, which is a lack of clotting platelets in the blood. People who suffer from severe hemophilia are in danger of bleeding to death, and are treated with a substance called Factor VIII, which stimulates the blood to produce more platelets. Leukemia is cancer of the white blood cells. Mytoid leukemia is the prescience of too many leukocytes, which are too immature to fight infections and crowd out the red blood cells. Lymphoid leukemia is a cancer of the lymphocytes. Treatment of leukemia requires the transfusion of new red blood cells into the affected persons body, and new, healthy white blood cells, as well as radiation therapy. THE LYMPHATIC SYSTEM The lymphatic system works alongside the circulatory system, primarily to regulate the amount of fluid that is distributed to the body. As the blood passes through the capillaries, some plasma bleeds out into the interstitial fluid. The lymph system collects this plasma, and takes it back to the heart for reintegration into the circulatory system. The Lymph nodes also facilitate the growth of the white blood cells, which protect the body against infection. Infections or illness cause the body to increase the number of lymph nodes, and their size. Some people can feel the swelling on their jawbone, or in their armpits. Lymphatic Defense System The body is an excellent growing place for many pathogens and other bacteria. The body defends itself by either refusing their entry, or attacking them inside. There are three methods of defense the body employs: The first is a physical barrier provided by the skin to stop entry of pathogens. The oil in the skin, and the acidity of sweat all are hostile to the life and reproduction of bacteria and pathogens. Cell Mediated Immunity is created by three types of white blood cells, and is the second level of defense. Macrophages, neutrophills and monocytes all work together to destroy pathogens. The later two utilize phagocytosis, swallowing the offending pathogens whole. Macrophages use phagocytosis, and swallow cells that have already been infected with pathogens, or with cancer. Specific Anti-Body Mediated Immunity, uses specific protein antibodies that are created either through exposure to the pathogen previously, or through genetic makeup in order to help rid the body of the infection. Lymphocytes are the active portion of the white blood cells that participate in the removal of diseases and are divided into B and T cells,

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the former of which matures in bone marrow, and the latter in the thymus gland, near to the heart. How do these cells know what to attack? Your body has a catalogue of what should be inside of it, and these cells have access to that catalogue. In addition, antigens, special receptor cells on the edges of pathogens are specific to the antibody attacking. The antibody enzyme latches directly onto the antigen.

B Cells function to create the specific antibodies required to thwart off the infection. The B cells split into memory B cells, and plasma cells. The plasma cells pump out massive amounts of antibodies to fight the infection, while the memory B cells wait into the blood stream to produce more plasma cells should a second wave of the pathogen become present after all the plasma cells and antibodies have been used up. T Cells facilitate the removal of macrophages which have become infected after destroying part of the pathogen. Helper T Cells recognize the presence of the antigen on the macrophage cells, and stimulate chemically the Killer T Cells, which puncture a hole in the cell membrane of the macrophage, destroying the infected cell. Supporter T Cells

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ensure that regular tissue is not destroyed by the Killer T Cells. Memory T Cells send new chemical signals if all the other T Cells have been used up and the pathogen remains. Blood Types Blood transfusions in early days were very unsuccessful, because scientists did not know that specific blood types carry different antigens to blood receptors. The prescience of the type A or type B antigens on the surface of the person’s blood cells determines the type of blood they have. The presence of Type A antigens means you have type A Blood, alike type B. Type A also contains anti-A antibodies in the plasma. When blood of different types comes together, it causes agglutination, or massive clotting of the circulatory system which leads to severe damage of organs and death. The table on the right summarizes human blood types. RH is another factor of blood type. People who do

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have RH antigens are considered RH positive, while people who do not are RH negative. In human pregnancy, if the mother is RH negative, and the father is RH positive, the child will likely be RH positive. While in the uterus, the mother’s body will be begin to develop RH antibodies, and on subsequent pregnancies, this can cause severe problems. Hemolytic Disease of the Newborn (HDN) is the destruction of a newborn’s red blood cells due to the attack of the RH antibodies on the fetus. Jaundice, a newborn condition is caused when RH has destroyed so much of the red blood cells that the liver has now begun to produce bilruben, a yellowish substance, in massive quantities. This tinges the newborn’s skin yellow, as the billruben flows through the circulatory system. This problem is medically solved by injecting RH negative women with a antibody preparatory inhibitor within 72 hours of the birth of her first child. Immune System Disorders Rheumatoid arthritis is the killer T Cells attacking the joints of the body, causing server damage, inflammation of the joints and a lot of pain for the individual. Drugs such as Tylinol can be taken to reduce the pain, and more severe disease modifying antiartheumatic drugs slow the overall progress of the system. Allergies are caused by an unreasonable response by the immune system. Immediate response usually occurs within thirty minutes of infection, and results in blood rushing to the area of contact, making it red and swollen. This also causes side effects such as runny nose, or watery eyes. Asthma, a chronic condition in North America, occurs when the bronchitis of the lungs become overly sensitive, and trigger massive spasms or coughing fits. Stimuli can be extremely simple, such as the inhaling of cold air, or the prescience of certain pollens. Asthma can be treated by anti-inflammatory drugs, which ease the suffering of the bronchitis openings. Delayed response to allergies is caused due to the creation of helper T cells, which take some time to create. These allergies can occur to the prescience of jewelry or certain cosmetics.

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THE HUMAN RESPIRATORY SYSTEM Cellular respiration is the main function of the human respiratory system and ensures that we, as humans are able to take in oxygen and expel carbon dioxide. There are two main requirements for respiration to take place: 1. Respiration must have enough surface area to take place at a speed to meet the body’s needs. 2. Respiration must take place in a moist environment. The stages of cellular respiration are as follows: 1. Breathing – involving two basic functions, inspiration (inhalation or breathing in) and expiration (exhalation or breathing out). 2. External Respiration – facilitates the exchange of oxygen and carbon dioxide in the air and blood. 3. Cellular Respiration – is a process that takes place in the cells that creates the energy sources required to facilitate cellular reactions utilizing the oxygen provided. STRUCTURE OF THE RESPIRATORY SYSTEM The lungs are the key component of the respiratory system, and are located deep inside the body, protected by the ribcage and the thoracic cavity. How does air come to the lungs? Well, air begins its journey at the nasal and mouth. Air usually enters via the nose, but can enter via the mouth when a rapid exchange is needed. The nasal cavity cleans the air, removing toxins and other bacteria. The nose is lined with little hairs known as cilia, which move foreign particles to the back of the nose for coughing or sneezing out. The nose also has cells that secrete mucus, which catch foreign cells within its sticky substance. Thin bones protect the back of the nose, turbinate, which increase the surface area for the cilia to be attached to. The heat from the blood in the nose and the mucus also serve to warm the air, and moisten it. The air must be warmed and moistened in order to protect the delicate structures of the respiratory system. The pharynx or the throat is the passageway air follows down to the lungs. The epiglottis is a thing flap of membrane that ensures that food and other particles that are going to the digestive tract do not go down the tube in to the lungs. The epiglottis does this by closing over the trachea, or the glottis, which is the windpipe. Food thus goes down the esophagus and into the stomach instead of into the lungs.

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The larynx, or vocal cords, regulates the pitches that can be created by your voice. During breathing, the cords are usually spaced very wide together. But, when you speak, they come together and the air that passes through causes them to vibrate. Longer vocal cords usually create lower pitches, while shorter ones create longer pitches. After passing the larynx, the air passes down the trachea, which is structured by strong semi lunar rings of cartilage. The open portion of the trachea faces the esophagus so that the former can contract, permitting the later to expand when food is swallowed. The trachea branches into two smaller pathways, the bronchi. The bronchi enter the left and right lungs, and have C-shaped cartilage rings, like the trachea, that provide support and stability to the lungs. The bronchi divide into bronchioles, tinier tubes. Both the bronchi and bronchioles contain cilia, tiny hairs that sweep the air through the respiratory tract, and also clean it. The lungs are surrounded by a double layer of membrane, known as the pleural membrane. The outside of the membrane is stuck to the chest wall, while the inter portion of the membrane attachés to the lungs. Fluid fills the space in between the membranes. This allows the lungs and chest to expand and contract uniformity, without causing tearing or friction between the membranes. At the end of each bronchiole are tiny sacs known as alveoli. This is where the actual gas exchange takes place. The wall of the alveoli, known as the alveoli wall, is filled with tiny capillaries, which connect the veins and arteries of the body togther. Oxygen and carbon dioxide can diffuse into the bloodstream directly through these capillaries. The arrangement of bronchioles and alveoli is kept relatively constant with elastic connective tissue between them. Lubricating film is also used to keep the alveoli from collapsing or from sticking together.

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BREATHING AND RESPIRATION In order to regulate air pressure and breathing, two different muscles are used. The diaphragm is a dome shaped muscle that separates the thoracic cavity from the abdominal cavity. The rib muscles exist between the ribs and extend down to the diaphragm. The Mechanics of Breathing Inhalation starts with the contraction of the diaphragm and the the rib muscles upwards and outwards. The size of the thoracic cavity increases, and the air pressure between the plural membranes of the lungs decreases. Since the lungs are sensitive to this pressure change, they begin to expand, and the difference in concentration of air particles from the outside environment and the inside of the lungs causes air to rush into the lungs.

Exhalation occurs in the opposite way. The diaphragm and the rib muscles expand decreasing the size of the thoracic cavity, and increasing the air pressure. The lungs contact, and the air pressure between the external environment equalizes, by air shooting out of the lungs.

Respiratory Volume How “much” air you can breath in and out, exhale and inhale, is calculated using a system known as respiratory volume. A spriograph (left) is used to show a person’s respiratory volume. Here is what some of the terms on it mean: • • Tidal volume is the amount of air that is inhaled and

exhaled during normal breathing in the body. Inspiratory reserve volume is the amount of air that can be pushed into the lungs after a normal breath (tidal volume).

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• • •

Expiratory volume is the amount of air that can be pushed out of the lungs after a normal breath (tidal volume). Vital capacity is the total lung capacity a person has. It can be calculated by adding tidal volume to either the expiratory volume or the inspiratory volume. Residual volume is the amount of gas that remains in the respiratory system. No amount of force can push this out: it remains there to ensure that the lungs and thoracic cavity remain inflated.

Gas Exchange and External Respiration External respiration is the transfer of oxygen and carbon dioxide between the capillaries and the alveoli. Because the capillaries are only one cell thick, diffusion can move oxygen and carbon dioxide particles across the membrane, because diffusion works with the concentration gradient (in other words, moves the oxygen and carbon dioxide to where there is a less concentration from an area where there is higher concentration). Oxygen is also transferred by way of facilitated diffusion, by special molecules that carry the oxygen across the cell membrane. This requires no additional energy, as the oxygen is still moving with the concentration gradient, instead it just increases the speed of the diffusion. After being exchanged here, the oxygen is transported to the cells, where it is again exchanged for carbon dioxide, which is brought back to the capillaries and the alveoli. The oxygen, as you learned previously, is carried by the hemoglobin. Approximately 99% of oxygen is carried by the hemoglobin, while the other 1% dissolves into the blood plasma and is carried using that method. Carbon dioxide, on the other hand, is carried through a variety of methods. 23% is carried by the hemoglobin, 7 percent is carried by the blood plasma. The other 70% is carried as bicarbonate ions (HCO3-). When carbon dioxide and water react, they form carbonic acid, H2CO3. As the carbonic acid enters the blood stream, a hydrogen atom disassociates from the carbonic acid and is absorbed into the hemoglobin. The bicarbonate diffuses into the plasma, and is carried to the lungs where this process is reversed, and the carbon dioxide diffuses through the capillaries into the alveoli and out of the respiratory system. RESPIRATORY HEALTH Briefly, are a couple ailments that can affect the respiratory system. Recall that the respiratory system, like the digestion system, exists in coordination with the external environment and are therefore susceptible to a number of ailments.

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Upper Respiratory Ailments • Tonsillitis is the viral or bacterial infection of the tonsils (located in the back of the pharynx. They can be removed surgically if breathing becomes impaired, or if they become super prone to infection. • Laryngitis is the viral or bacterial infection of the larynx (vocal cords). Usually this results in the cords being unable to vibrate normally, causing speech to be difficult, and the throat to be sore. Lower Respiratory Ailments • Bronchitis is the inflammation of the bronchi, due to a high volume of mucus (filled with foreign particles) needing to be coughed out regularly. Acute bronchitis usually resolves quickly, but chronic bronchitis is not curable, and is usually caused by the loss of the cilia, the hair that scrubs the air and removes foreign pathogens. Chronic bronchitis can be managed with various medications, exercise and staying away from smokers (or quitting smoking yourself). • Pneumonia is fluid filling the alveoli, interfering with gas exchange and thus starving the body for oxygen. Lobular pneumonia affects a specific region or lobe of the lungs. Bronchitis pneumonia interferes with various particles throughout the lungs. • Pleurisy is the infection and swelling of the membranes that surround the lungs, and is usually accompanied by sharp chest pain. It can be caused by bacterial or viral infections, a blood clot in the lungs, or cancer. • Emphazema is the reduction in elasticity of the alveoli, which reduces the speed at which gas exchange takes place, laboring breathing. Various medications, such as inhalers or low-flow oxygen tanks can assist in making breathing easier. There are also experimental surgeries known as Lung Volume Reduction surgery, which take out the affected parts of the lung, and increase the efficiency of the parts that are working well. • Cystic Fibrosis is caused by a rogue gene that causes the cells in the lining of the lungs to not function correctly, creating too much mucus. Particles that are trapped by the mucus cannot be expelled, and therefore result in continued infection. Currently, cystic fibrosis is treated through mucus thinning medications. Experimental gene modification treatments are also being worked on. • Asthma is the over-sensitization of the bronchi and bronchiole in the lungs to certain triggers, for example pollen, dust or cigarette smoke. When these are breathed in, the tubes become inflamed and result in swelling or an asthmatic attack where the person cannot breathe. Dry and forced inhalers work to reduce swelling in the bronchi and bronchiole by either forcing gaseous chemicals down the throat that relieve the swelling, or having the person inhale rapidly to force a powder down. There are also nebulizers which are masks that are worn over the face to administer the drug by mist. • Lung cancer is the rapid multiplication of abnormal cells in the lungs, leading to tumors or carcinomas. Carcinogens are substances that are cancer causing, such as cigarette smoke, exposure to asbestos or longer term exposure to radon, a heavily gaseous radioactive element found in rocks and soil that collects in buildings. Instruction on Concepts, Problems and Applications 36

CELLULAR RESPIRATION Cellular respiration is the process by which glucose is oxidized into carbon dioxide, via the chemical removal of hydrogen ions and elections from glucose, releasing carbon dioxide and producing water. Cellular respiration is the opposite process to photosynthesis, which occurs through the addition of hydrogen ions and elections into glucose. A graphical representation of cellular respiration is provided to the right. The summary equation for cellular respiration is as below: C6H12O6(s) + O2(g) → 6CO2(g) + 6H2O(l) + energy (ATP) There are three different methods that organisms can utilize for cellular respiration, some of which have the same steps involved. Organisms that utilize oxygen, known as oxic organisms, use aerobic cellular respiration while organisms where oxygen is not required use anaerobic cellular respiration. The third process, for releasing energy from food sources is called fermentation. Yeast, and the bacteria that sours milk, are two examples of fermentation. AEROBIC CELLULAR RESPIRATION STEPS Aerobic Cellular Respiration has the ultimate goal of transforming the high energy elections from the glucose to a carrier oxygen molecule. It does this through four distinct processes, which shall be summarized here and then further explained in the next bit. Glycolosis does not require oxygen to commence (it is actually an anaerobic process, so both aerobic and anaerobic organisms perform it). Glycolosis is the chemical breakdown of glucose into two three-carbon pyruvate ions. Glycolosis generates a small amount of ATP, the energy source utilized by bodily cells. In anaerobic organisms, the leftover pyruvate from glycolosis proceeds to fermentation. In aerobic organisms, the next step from glycolosis is an entrance into the Krebs cycle, through the loss of a carbon atom, which bonds with an O2 molecule to form carbon dioxide. It also loses a hydrogen atom, and gives it to NAD+, which become NADH, a transport molecule. The loss of the carbon ion permits the pyruvate to bond with Coenzyme A and enter into the Krebs cycle via NADH. Within the Krebs cycle is to transform the power of the carbon atoms into power chemicals NADH and FADH2. Finally, the Krebs cycle provides high energy elections for the Election Transport System, which generates a high volume of ATP. Confused? We were too. Lets take a look at this in detail…

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Step 1: Glycolosis Glycolosis occurs outside of the mitochondrion of the cell, in the cytoplasm. As you learned above, glycolosis splits the glucose molecule (a six carbon molecule) into two three-carbon pyruvate molecules. 2 ATP molecules are required in order to make this reaction take place, as glucose actually needs energy added to break in two. However, at the conclusion of glycolosis, four ATP molecules are gained, leading to an overall increase of 2 ATP molecules. Step 2: Coenzyme A Reaction & Entrance into the Krebs Cycle Pyruvate undergoes one additional reaction before entering the Krebs cycle. Pyruvate loses a carbon atom and a hydrogen atom. The carbon atom leads to bonding with an oxygen molecule, forming carbon dioxide, which is then expelled as waste. The hydrogen bonds with a NAD+ to form NADH. Coenzyme A and pyruvate form acetyl CoA, which then enters the Krebs cycle. Step 3: The Krebs Cycle The Krebs cycle starts off with a six-carbon molecule, two of the carbons being provided by the acetyl CoA, from the previous step. As sown in the figure, a six carbon molecule moves around the Krebs cycle, losing a carbon each time to move NAD+ to NADH. 2 molecules of carbon dioxide are also produced as waste. During the Krebs cycle, a further 2 ATP molecules are produced. Step 4: Election Transport Election transport is the final stage in aerobic cellular respiration. In the mitochondria, high energy elections are passed through a chain of election carrying molecules. Each time the election is passed, a small amount of energy is released, in the form of a simple hydrogen pump, which helps push the molecules across the intermembrane space (space between the two membranes of the mitochondrion). This creates a hydrogen ion concentration gradient. The energy of the concentration gradient is then harnessed to bond a phosphate group to ADP and form ATP. This is called chemiosmosis and creates thirty-two ATP molecules during each transport of the elections. Oxygen is the final election receptor, and in this capacity is the only one that requires oxygen in the whole aerobic breathing process.

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The below image summarizes aerobic respiration within a cell:

Oxygen’s Importance Remember that oxygen is the key component of aerobic respiration. Even in such a small capacity, being the last election receptor, the election transport system, and subsequently the Krebs cycle could not take place without it. How important is oxygen? Well, without it, we would only form 2 ATP molecules. With oxygen, we form thirty-six. The flow chart to the right summarizes the production of ATP through aerobic cellular respiration.

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ANAEROBIC RESPIRATION Anaerobic Respiration works virtually the same as aerobic respiration, except that it does not include the Krebs cycle, and uses a different receptor then oxygen at the end of the election transport cycle. For this reason, it is highly inefficient, and only produces 2 ATP molecules, due to gylcolosis. FERMENTATION For organisms that cannot take in oxygen, or for tissues in the human body where oxygen is not present in large enough quantities, fermentation takes place. Fermentation includes glycolosis and two reactions that reduce NADH to NAD+ by reducing pyruvate to other compounds. There are two types of fermentation. Lactic fermentation and ethanol fermentation. Lactic Fermentation During extraneous exercises, where your muscles are without oxygen for times, or have inadequate oxygen sources, your muscles produce lactate, by synthesizing pyruvate to a molecule called lactate (lactic acid) through NADH. The resulting NAD+ is recycled to continue this process. This builds up an oxygen debt, as your pyruvate cannot be broken down fast enough by the Krebs cycle or the election transport system. The build up of lactic acid leads to fatigue and cramps in your muscles until oxygen is present again, and the oxygen is converted back to pyruvate. Ethanol Fermentation Ethanol fermentation is used by organisms utilizing anaerobic respiration. It is also utilized in baking, with the yeast found in many baking products. Barley, sugars and other ingredients are also fermented with this process to produce beer. Depending on the organism, other things then lactic acid and ethanol can be produced during fermentation. Ethanol fermentation can also be used to produce fuel. Today, many manufacturers are converting to partial ethanol usage, in order to save on gasoline.

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PHOTOSYNTHESIS Photosynthesis is the transfer of energy from sunlight into chemical energy. Photosynthesizing organisms are able to produce about 1.4x1015 kg of energy-storing glucose yearly. Other organisms such as humans depend on the abilities of photosynthesizing plants in many ways:

The basic reaction of photosynthesis utilizes the following formula: 6CO2(g) + 6H2O(l) + energy → C6H12O6(s) + O2(g) The reaction itself may seem simple, but for the arrow to go from carbon dioxide and water to glucose and oxygen, requires over 100 distinct reactions. Overall, these reactions can be classified into two categories. In Light-Dependent Reactions, solar energy is trapped and used to produce ATP and NADPH. In Light Independent Reactions ATP and NADPH are used to reduce carbon dioxide to glucose. The Light Dependent Reactions of Photosynthesis

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The Light-Dependent Reactions of photosynthesis result in different pigments within the plant absorbing different wavelengths of light.

Photosystems are arrangements of the different pigments that take in light, and their connection to send the absorbed energy to an electron absorbing chlorophyll or a reaction center where an election becomes excited and passes off to an election receiving molecule. A water molecule splits and replaces the missing election from the reaction center (and the leftover oxygen from the reaction is excreted by the plant). The election that went away is carried through its own election transport system where at each transport mechanism, the election releases a precise, small amount of energy that pushes it through the thylakoid membrane to the area inside of the thylakoid. As this occurs, energy is released to begin the synthesis of ATP. Instruction on Concepts, Problems and Applications 42

The next step, chemiosynthesis takes place in the thylakoid, where the movement of the hydrogen ions causes a concentration gradient that serves to release ATP molecules. The Light Independent Reactions of Photosynthesis When an ample amount of NADPH and ATP occur in the stomata and the chloroplasts, the energy goes through the Calvin-Benson cycle to form glucose. The Calvin-Benson cycle can be summarized as follows: The first stage is to fix carbon dioxide, where the carbon from the carbon dioxide is bonded to another molecule in the stomata called ribulose bisphosphate. The resulting six-carbon compound immediately breaks down into two three carbon compounds The second stage is to reduce. The two three carbon compounds are activated by ATP then reduced by NADPH resulting in PGAL. (PGAL is short for glyceraldehyde-3-phosphate.) Some of the PGAL is used outside of the cycle to synthesize glucose, while other portions of it move to stage three. The third stage is to use PGAL to reform the four carbon molecule ribulose bisphosphate. The Calvin-Benson cycle must be completed six times in order to synthesize one molecule of glucose. Of the 12 PGAL molecules created during six cycles, 10 are used to reproduce ribulose bisphosphate and two are glucose.

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MUSCLE CONTROL The muscle cells work to convert chemical energy from cellular respiration to kinetic energy, the energy of motion. There are three different types of muscle cells. Smooth Muscle Cells are long and tapered at each end. Their contractions are involuntary; you cannot control your smooth muscles. They are found in the stomach, many blood vessels, and in the iris of the eye. In each location, smooth muscle is responsible for controlling the shape and size of the muscles. Although contractions of the smooth muscle are slower then those of the skeletal muscle (see below), smooth muscle can contract for much longer without fatiguing. Cardiac Muscles are unique to the heart. They are tubular and strained and only have one nucleus throughout. Contractions are involuntary. Skeletal Muscles are what we think of when one says muscles. They control the movement of the human body, and are voluntarily moved. With over six hundred throughout the human body, skeletal muscles can produce a wide variety of movements. Multiple nuclei control the large and long series of a muscle and a great amount of energy are needed to run skeletal muscles. This image below summarizes the three different types of muscles.

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SKELETAL MUSCLE The main functions of skeletal muscle are as follows: • Support and Straighten the Body. Skeletal muscles go against the force of gravity, and help us to stand upright. • Make the Bones Move. Skeletal muscle contractions help to move our bones and hence cause movements in our arms, legs and facial expressions among others. • Maintain constant body temperature. Skeletal muscle contractions result in ATP breakdowns, releasing significant energy in the form of heat into the body. • Protects the Bonds, and Connects the Joints. Skeletal muscle helps protect the bones by providing a pad for the bones to rest on. As well, the tendons of the skeletal muscle Skeletal Muscle Cooperation Muscle contraction results in a shortening of the muscle – which exerts a pull (not a push). The work of the muscle is done during its contraction, when it is not contracted, the muscle is relaxed. In order to provide a force to contract one muscle, another must relax. Muscle contractions, therefore, are always done in pairs, one muscle contracting while the other is relaxing. A sample image of the bicep illustrates this point to the right. Skeletal Muscle Fibers Each muscle in the body lies along a bone, with two thick tendons on either end connecting the muscle to different bones. Muscle fibers, the main portion of the skeletal muscle, are organized into many bundles, with layers of connective tissue wrapping around them, and with connective tissue wrapping around the other connective tissue, an then a protective layer wrapping around the muscle itself. Blood vessels run between the fibers of the muscles,

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providing power and oxygen for the muscles, and taking the carbon dioxide away. Nerves near to the blood vessels trigger contractions. Most of the volume of the muscle fiber comes from the myofibrils, and the thinner myofilaments. The rest of the volume consists of mitochondria. The below table summarizes the muscle tissue.

How Muscle Fibers Contract Skeletal muscle contraction is due to the efforts of two myrofibrils, actin and myosin. Actin is a thin filament with two strands of protein intertwined that looks alike two sets of balls strung together and wrapped around one another. Myosin is two thin tubes twisted together, and at the end it has a head like protrusion extending from either tube.

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During a contraction, the heads of the myosin myrofilament touches the actin myrofilament and moves in the direction of the contraction. This causes the actin to move as well, because it is chemically bonded with the myosin. As each head touches the actin and moves down, ATP is released. This is known as the sliding filament model and is depicted below:

The Z line is an anchor to each myrofilament, and as the myosin pulls the actin along, the z line anchor is pulled too, contracting the whole muscle uniformly.

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Calcium ions (Ca++) regulate the muscle contractions. Binding of the myosin heads to the actin myrofilamnets cannot take place without a high amount of calcium, because without it tropomyosin forms – a natural inhibitor for the chemical bonds that need to take place in order for contraction to occur. The complex of tropomyosin shifts away from the areas where the bonding sites are located in the presence of high calcium intake. Creation of Energy Required for Muscle Contraction ATP is acquired through three methods, creatine phosphate breakdown, aerobic cellular respiration and fermentation. The first and third methods can be completed without oxygen, while aerobic cellular respiration requires oxygen to take place. Creatine phosphate is a high energy compound that is made in the muscle while it is at rest. Creatine phosphate is activated with the sliding of the filaments, and provides about eight seconds of high energy burst. Creatine phosphate forms ATP through the reaction shown on the right. Aerobic cellular respiration can occur when the delivery of oxygen commences to the muscle cells, but also when oxygen is stored in the myoglobin, a compound alike hemoglobin that is synthesized in the muscle cells. Glycogen and fats can also be stored in the muscles, and therefore fibers can use glucose and fatty acids from the stores to produce ATP. Fermentation is the production of lactic acid from glucose to form ATP. Fermentation changes the pH of the muscle, and after a given amount of time, leads to cramping and fatigue. An oxygen debt occurs, causing the person to continue to breathe heavy after exercise. MUSCLES AND HEALTH Muscles are susceptible to a variety of injuries including simple lack of use. Atrophy is a reduction in size, tone and power of a muscle. People who do not exert a muscle, or stop exerting a muscle even for a short period can experience atrophy. Over time atrophy can be permanently damaging. Hypertrophy is the opposite, the enlargement of a muscle due to regular exercise done upon it.

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Common Ailments of Muscles The below table summarizes some common ailments of muscles:

Muscle Twitch Electrolytic stimulus can take place on a muscle and result in a systematic contraction. A muscle will not contract until the exact amount of electricity required to pass its threshold is exerted, and then the muscle contracts then relaxes. (See the figure to the left). Stimulus that is replied repeatedly, not giving the muscle time to relax, results in an increased contraction until the tetanus point, where the muscle can no longer contract, and then relaxes at fatigue. Slow Twitch and Fast Twitch Different muscles twitch at different speeds. Slow twitch require a higher amount of electricity to twitch, but have a greater endurance time. Fast twitch muscles require less electricity, but fatigue quickly.

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THE EXCRETORY SYSTEM The excretory system seeks to maintain the volume and composition of the various fluids within the body. Waste within the human body is any substance that is produced within the body in excess, for example sodium (Na+) ions, chloride (Cl-) ions and hydrogen ions (H+). Wastes, in large quantities can post a risk to human health, particularly those types of waste that have an extreme pH (either highly acidic or highly basic). The excretion system is the apparatus which removes these wastes from the body. It works to separate them from the bodily fluids, package them appropriately for removal, and then secrete them back into the external environment. ANATOMY OF THE EXCRETORY SYSTEM Almost every human has two fist shaped organs known as kidneys, located in the small of their back beneath a thick layer of protective fat. Urine, the product of the kidneys, is released into two 28cm tubes known as ureters and down through them via peristalsis to the urinary bladder. Drainage of the bladder (in liquid form) is handled by two pyloric sphincter muscles, both of which must be relaxed in order for excretion to occur. The first is controlled involuntarily by the brain. The second we learn to control in childhood. Urine is secreted from the body via the urethra. The Urethra is 20 cm long in males, and combines with the Vas Deferens (of the reproductive system) in order to exit the body into the external environment. In females, the tube is only about 4 cm long and has a separate opening from the reproductive tract. The Kidney The kidney begins with a flap of tissue that leads to the renal pelvis, an apparatus with cap like extensions that receives urine from the renal tissue. This tissue is divided into two sections, the renal cortex and the inner renal medulla.

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Embedded within the renal cortex and the medulla millions of structures known as nephrons. The nephrons are closely associated with a group of blood vessels that filter various substances from the blood in order to prepare for waste production. Nephrons are organized as follows: 1. The Filter: the filtration structure is also known as the Borman’s capsule, and within it the renal artery splits into a fine network of capillaries known as the glomerulus. The capillaries have walls that are impenetrable to larger particles, save red blood cells. While it prevents larger particles from seeping through, water, urea, small molecules and ions are able to pass through at will. The filtered substances that proceed from the Borman’s capsule are called filtrate. 2. A Tubule. The Bowman’s capsule is connected to a tubule known as the Loop of Henle. Its function is similar to the small intestine, absorbing nutrients that could be useful to the body. It also secretes substances into the surrounding tissues. 3. The final Duct. The Loop of Henle empties into a duct known as the collecting duct. The duct serves to collect the water that was not already reabsorbed into the body. The fluid that is left is now called urine.

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URINE PRODUCTION There is a four step production method to urine production. It is, as follows: 1. Glomerular Filtration moves water and solutes, except proteins, from blood plasma into the nephron. 2. Tubular Reabsorption is the removal of useful substances from the filtrate, and their subsequent return to the blood. 3. Tubular Secretion is the removal of additional wastes from the blood into the filtrate. 4. Water Secretion removes water from the filtrate to maintain body systems. Two factors contribute to the forced filtration (glomerular) are the permeability of the membranes: their size and shape ensure that only desired particles can get through them back into the bloodstream. The second factor is blood pressure. The pressure within the glumeulus is about four times higher then the other locations in the body, leading to the forced filtration. Proximinal Tubule About 65% of the filtrate that passes through the proximinal tubule and the loop of Henle is passed back into the body. The proximinal tubule is filled with mitochondria that use their ATP production process in order to force Na+ and glucose ions back into the bloodstream via active transport. Negative ions pass over passively, attracted to the positive Na+ ions. Water also moves over via osmosis. Loop of Henle The Loop of Henle is responsible for the reabsorption of water and other ions from glomerular filtrate. As the loop of Henle swirls down towards the lower medulla region, the saltiness of the external environment increases, and the water simply diffuses (via

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osmosis) through the semi permeable membranes of the Henle into the medulla region. The membrane of the lower portion of the Loop of Henle is not permeable to ions however, it is not until the loop curls back up that the ions can be diffused though the membrane into the kidney. As the filtrate reaches the highest thickest point of the loop of Henle, the ions are remove3d via active transport.

The transport of ions out of the loop of Henle helps to replenish the salty environment in the medulla, ensuring that the water can be reabsorbed. It also reduces the concentration of the filtrate. Distill Tubule The distil tubule is responsible for the reabsorption and secretion, as to the body’s needs. The body “tops up” on nutrients and other ingredients it requires to live (reabsorption). It also dumps excess (secretion). Collecting Duct As the filtrate enters the collecting duct, it is still highly concentrated with water. Depending on the dehydration level of the 53 SHR – Biology 20

person, the concentration of the ions and the saltiness of the surrounding deep medulla that the collecting duct is held in, increases or decreases to proportionally increase or decrease the amount of reabsorpiton and collection of water via osmosis. Summary What is left is a filtrate that is about 1% of its original volume, and is now called urine. The below table summarizes the different portions of the nephron.

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MAINTAINING THE EXCRETORY SYSTEM The Kidney’s maintain the excretory system by controlling the amount of water that is absorbed. Osmotic pressure refers to the force generated by water in the concentration gradient. The kidneys ensure that enough water gets into the body systems by regulating the osmotic pressure. When you are water deficient, osmoreceptors within your brain become aware of the situation and send ADH (antidiuretic hormones) through the bloodstream to the kidney, where the permeability of the distill tubule and the collecting duct is increased, permitting increased water retention. It also works in reverse, with a reduction in the production and release of ADH.

Salt Reabsorption The hormone aldostone regulates the kidneys in such a way to control the reabsorption of Na+ ions by stimulating the distill tubule and the collecting duct to retain more sodium ions. Maintaining Blood pH Blood pH is regulated by three things – the acidbase buffer system (involving carbonic acid and bicarbonate ions) where the reaction is shown on the left, and a system that involves breathing rate and the generation of carbon dioxide. The Kidneys work with these two systems in a more powerful way, secreting H+ ions to make the blood more basic, and HCO3- ions to make the blood more acidic. 55 SHR – Biology 20

Renal Insufficiency Renal insufficiency means that the kidneys cannot sustain balance in the body due to damage to their nephrons. Some causes of nephron damage are: • • • • • • • kidney infection high blood pressure diabetes mellitus trauma from a blow to the lower back or constant vibration from machinery poisoning (either from skin contact, inhalation of fumes, or ingestion of contaminated food) by heavy metals such as mercury and lead or solvents such as paint thinners atherosclerosis (which reduces blood flow to the kidneys) blockage of the tubules

Kidneys can work with severe problems. 75% of the nephrons need to be seriously damaged before homeostasis cannot take place, and a person must go on the blood cleansing process dialysis. Dialysis Dialysis is the movement of dissolved substances through semipermable membranes from areas of higher concentration to areas of lower concentration. Hemodialysis uses an artificial membrane in an external device, an artificial kidney in other words, to cleanse the blood, which runs out of a person’s arm through a series of tubes through a machine. Peritoneal Dialyses uses the lining of the intestine to perform the dialysis, an area called the peritoneum, which is rich with capillaries.

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ENERGY TRANSFER IN THE BIOSPHERE Organisms utilize the transfer of energy to remain alive. While most organisms utilize cellular respiration in order to release energy. The release of carbohydrates occurs within the cellular structure of animals, plants and humans which allows us to remain alive. The chemical equation for cellular respiration is as follows:
C6H12O6(s) Carbohydrates (sugars and starches) + 6O2(g) + oxygen → 6CO2(g) → carbon dioxide + 6H2O(l) + water + energy + energy

Some types of organisms, such as plants, algae and some bacteria can utilize the sun’s energy in a process known as photosynthesis in order to create the energy required to live. The equation for photosynthesis is:
6CO2(g) + 6H2O(l) carbon dioxide + water + light energy + light energy → C6H12O6(s) + 6O2(g) → carbohydrates + oxygen (sugars and starches)

Organisms that utilize photosynthesis are known as producers (or, scientifically autotrophs) because they create their own energy to survive. Other organisms that eat plants or animals to survive are known as consumers (or, scientifically heterotrophs), because they take the energy of other organisms in order to live. ENERGY ENTERS THE BIOSPHERE The Sun Provides Energy You recall, of course, that the sun is the source of energy for all producers that grow on the earth’s surface. Energy from the sun goes many places, as summarized by the figure, right, and by the below. On average, about thirty percent of the radiant energy from the sun is shone directly back into space. Albdedo is a term that refers to how much energy is reflected back into space in any given spot on the Earth. Although in different areas, Earth’s Albedo varies from spot to spot, with it being highest in thick cloud cover, or when there is light colored reflective surfaces, and it being its lowest over forest canopies which suck in the radiant energy. Approximately 19 percent of the energy is absorbed by gasses and liquids, such as water vapor and carbon dioxide in the atmosphere. Some of this energy heats the atmosphere, and some radiates back into space.

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The other 51 percent of the energy reaches the surface, warming the land and the water on earth. Some is absorbed, and other soaks back into the atmosphere and back into space. Only about one or two percent overall actually reaches the producers on the ground. However, the impact of this small percentage is highly significant. Producers create over 150 billion tons of matter each year. This matter sustains the rest of the life on earth. Life Under The Sea Scientists, diving deep under the Galapagos Islands wanted to discover more about the deep sea vents at 2500 meters below ground. What they discovered was remarkable: signs of deep sea life. Because the organic life at that level had no access to light, they could not utilize photosynthesis to produce their own energy. Instead, small bacteria that lived on the creatures split the hydrogensulfide molecules that spewed from the deep sea vent. This gave them the energy they required to live, with sulfuric acid as a byproduct (instead of oxygen in photosynthesis). Scientists were marveled, and named the process they’d discovered chemosynthesis. Chemosynthesis does not only occur underwater. In the soil that we tread on, lives a similar type of bacteria that converts the ammonia to a nitrogen based compound. This type of bacteria is called nitrifying bacteria. Consumers We know that only producers can produce energy for themselves through the sun. Consumers are creatures that eat other creatures in order to gain energy for themselves to live. Primary consumers are usually herbivores, because they are the first eaters of plants. Secondary consumers are carnivores which usually eat herbivores. Tertiary consumers are carnivores that eat herbivores and other carnivores. Decomposers are creatures who obtain their energy by consuming the dead material of organisms, such as their feces or, when they die, their bodies. By consuming them, decomposers slowly return the mater they consume back to the biosphere and ensure that the producers have matter to utilize when creating energy. In essence,

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decomposers are the matter recyclers of the ecosystem.

Energy in the Biosphere Earth is a closed system, which does not permit matter to enter or leave it. Due to the process outlined above, our Earth’s natural biosphere ensures that matter is recycled so that it can be reused infinite times. While matter is recyclable, energy is not. Energy enters the biosphere on a one way path only. Recall the first law of thermodynamics from your previous studies “Energy cannot be created or destroyed. It can only be converted from one form to another or transferred from one object to another.” Energy entering the biosphere is utilized by organisms in order to perform work. The energy that is used does not “disappear”, but is simply converted into another form of energy and transferred from one object to another (for example, energy is transferred from a creature as it moves across the land to the land). However, this conversion process is not 100% effective. Some energy is always lost in the environment. For example, when you drive in an automobile, energy is transferred from the fuel into the kinetic energy to move the vehicle, sound energy from the engine and some thermal (heat) energy that is lost randomly into the environment. This relates to the second law of thermodynamics which is “With the conversion of energy, there is always less energy left available for useful work”. The second law of thermodynamics also relates to cells. Cells require energy constantly to continue their operations. With the loss of available energy, the cells cannot continue their operations, and cease to life (they die). That is why producers are so important to the biosphere, because they are able to produce the energy that other organisms cells need to survive. ENERGY TRANSFER WITHIN THE BIOSPHERE Ecosystems Within the Biosphere An ecosystem (or ecological system) is the combination of the organisms that live within an area, and the physical environment of the area. An ecosystem is the combination between the living (biotic) and non-living (abiotic). The living component of the ecosystem consists of organisms, and their products and wastes whereas the non-living component is the water, inorganic substances such as minerals and the sunlight within the area. Within an

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ecosystem is an intensely complicated transfer energy transfer mechanism. Understanding this transfer is a major component of ecology. Relationships between organisms that consume one another for energy are described as tropics. The flow chart (left) demonstrates these relationships. Tropic levels identity organisms on the basis of how they get the food they need to eat. We’ve already learned the classification of “herbivore” and “carnivore”. The flowchart also shows the classifications of “primary consumer”, “secondary consumer” and so on. However, Tropic levels introduce a new element into the equation. They also explain the energy that is transferred throughout the ecosystem. The first tropic is given to creatures who create the chemical energy in order to feed all other tropic levels. All higher levels consist of organisms that feed on each tropic below them. Decomposers can feed on any tropic level. Food Chains and Webs You might notice that the tropic levels, and their subsequent classifications are much alike food chains that you’ve seen in previous studies. The concept of the food chain was originally accredited to Charles Elton who set out from the Oxford University in England in order to study arctic creatures that lived off the coast of Norway. Food Chains show linear progressions of food and energy transfer between organisms. (A sample food chain is shown on the right hand side). Elton realized quickly however, that food chains could not adequately describe the complex relationships of energy transfer. A Food web allows for a more realistic interpretation of the transfer of energy and food within the ecosystem. Food webs can only extend through so many tropics, due to the second law of thermodynamics. Loss of energy in each tropic ranges between 80-90 percent. (In other words, when energy is transferred from one tropic to another through the consumption of an organism, only 10-20% of the energy within the organism is actually transferred). Ecologists refer to the “Rule of 10” which states that, for general use, only 10% of energy is transferred in the tropics. Elton also developed another key concept with respect to food webs and chains. He also noted, through the high visibility of population numbers in organisms in the tundra, that as the tropics grew higher and higher, the number of animals grew lower and lower. This is sensible, because of the

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Rule of 10. The Rule of 10 can be applied when we say that in order to keep an animal alive in a tropic one degree higher then the one below it requires the energy of 10 animals in the tropic below. This explains why the populations become smaller as you raise up the tropic scale. Biomass Pyramids Biomass is the measure of dry mass (usually in g/m2) that an organism or group of organisms have. Biomass has also been worked into the structure of the Eltonian pyramid to properly identify the differences in mass between the organisms of each tropic level. Hence, a Biomass pyramid is a structure that incorporates the tropic levels, and also gives estimations on the total biomass of each tropic. A biomass pyramid is pictured below:

An inverted biomass pyramid is generated in many undersea ecosystems. For example, when you compare the biomass pyramid of the phytoplankton and the zooplankton the biomass of the phytoplankton is, at times, far less then that of the zooplankton in the tropic above it. How is this possible? The reproductive systems of the phytoplankton give them the ability to be reproduced fast enough to be immediately consumed by the zooplankton, and hence enough energy remains to keep the ecosystem working, while still resulting in an inverted biomass pyramid. Energy pyramids remove the exception of the zooplankton, because there cannot be less energy in a tropic lower then another tropic. Hence, energy pyramids are always upwards, and never inverted. An example of an energy pyramid is shown to the right hand side of this page. 61 SHR – Biology 20

CYCLES OF MATTER On a hot day, the human body perspires in order to cool itself. The water that is created through the bodies pores is cycled back into the environment, either through evaporation off the skin or by run off into a water culvert. Consider where the water may go when it has reentered the biosphere. Perhaps it went into the atmosphere, and rained down during a storm? Perhaps after this storm it ran off into the drinking water system that we use. Consider where the water that you release today goes in the environment. The cycle that water and other chemicals take through the biotic and abiotic components of the environment is called the biogeochemical cycle. This section will instruct you on various cycles in the ecosystem. THE HYDROLOGICAL CYCLE The hydrological cycle is the scientific name for the water cycle, which deals with all phases that water on earth goes through. The hydrologic cycle helps to connect ecosystems across vast distances on the earth. Approximately 97% of water in the biosphere exists in liquid form, due to water’s relatively high boiling point. Water vapor exists in the atmosphere, primarily due to evaporation. Water vapor is also a greenhouse gas, and remains in the atmosphere; as it rises it moves towards the poles and distributes heat away from the equator. Liquid water, in the seas also works to spread out the heat evenly throughout its body. Warmer water can also heat the air, and moderate the temperature of nearby landforms. Water at the Chemical Level Specific reasons water can transfer thermal energy, and dissolved minerals are: • Water is a universal solvent. • Water has a relatively high boiling point and melting point. • Water has special adhesive and cohesive properties. • Water has a high heat capacity. What makes water an excellent carrier of dissolved substances? A water molecule, consists of two hydrogen atoms covalently bonded to an oxygen atom. The hydrogen end

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of the molecule gives off a slightly positive charge, while the oxygen end gives of a slightly negative charge. This is referred to as a polar molecule, because it has differentially charged sides (poles). Because water is a polar molecule, it can easily attach itself to other water molecules via an attraction of opposite poles. For example, the negative pole of one water molecule attracts to the positive side of another water molecule. This forms a weak bond known as a hydrogen bond. The structure of the water molecule, including its polarity and the fact that it can readily form a hydrogen bond makes it very useful in dissolving both molecular and ionic compounds. The hydrogen bond itself is very weak. When water is in a substance form, individual hydrogen bonds between molecules break and reform rapidly. However, when the number of molecules of water and the number of hydrogen bonds formed increases, he overall strength of the substance increases rapidly. Because the bonds can break and reform rapidly, water cannot boil until all the bonds have been broken. This unique property of the hydrogen bond helps us to explain why waters boiling point is so high when compared to other substances which do not form hydrogen bonds. The unique properties of hydrogen bonding also explain water’s density. Unlike most substances, water has a lower density in frozen form then in liquid form. When water freezes, the hydrogen bonds expand, holding the structure together in a crystal formation (see the figure on the right). Likewise, when water melts, the structure compacts as the crystal bonds break down. Water’s point of maximum density is 4ºC. When water is melting, it heats up and slowly becomes denser until it reaches this temperature. When it hits four degrees, the warmer water sinks below, and cooler water from above is heated. Subsequently, the opposite process occurs when water freezes, with cooler water sinking as it becomes less dense. Water Within the Ecosystem and Biosphere Water has interesting and positive consequences to organisms within the ecosystems. As water rises and sinks, it cycles dissolved nutrients and oxygen through it. Water that penetrates around rocks and other solid landforms, and then freezes weathers the landforms releasing sediment, sand and other dissolved nutrients for use within the ecosystem. In addition because solid water is less dense, it can freeze overtop of liquid

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water, insulating it and preventing aquatic life from freezing or being frozen into a solid form. Cohesion is another unique property related to water’s hydrogen bond. Cohesion keeps water molecules tense and stuck together, and permits many small insects to “walk on water”. It also forces debris and other nutrients to the surface, permitting easier access to them by aquatic creatures. Adhesion permits water molecules to be attracted to other molecules. In a plant, the phloem and xylem are responsible for transporting nutrients up to the leaves for photosynthesis and then transferring the sugars created in photosynthesis to feed the rest of the plant. Although the sugars fall through the phloem via gravity, how does the xylem raise the water and nutrients up? Adhesion permits the water molecules to bond together with the nutrients taken in by the roots of the plant. Because the water molecules also have cohesion, transpiration removes the water molecules from the plant, causing other molecules to rise and take their place. Together, cohesion and adhesion permit water and nutrients to rise up the xylem into the leaves. Water also has a high heat capacity. This means that water requires a relatively large amount of energy to change its temperature, when compared to other substances. On a organism level, this permits organisms with a higher water level in their bodies to maintain a more moderate, constant, internal temperature. In a larger scale, water bodies help regulate and moderate temperatures of the land masses they are adjacent. Water also permits surface currents to distribute heat from the warm equator region to heat higher latitudes. Uses of Water Living organisms depend on water and the hydrologic cycle daily. More then 50% of all animal and plant tissue is comprised of water. 70% of the adult human is water, while 95% of the radish, a plant, is comprised of water. Water loss and gain, are parts of daily life for many of earth’s organisms. Water is also essential for human consumption, for drinking, washing, bathing and cooking. It is also used for crops and livestock. Water’s importance to Alberta is clear: with two of our largest natural disasters being draughts in the prairies during the 1930s and 1980s. If global warming is occurring, then we may see an increase in quantity and severity of draughts in the future. Water quality is also a key issue. Water that cannot be reused, due to contamination, is useless to humans and cannot be released back into the environment without causing significant damage to the ecosystem.

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BIOGEOCHEMICAL CYCLES Consider the relation between autotrophs (organisms that create their own food) and heteotrophs (organisms that consume autotrophs). Could the former survive without the later? The answer is no, because heterotrophs provide nutrients required in order for autotrophs to make food. Throughout ecosystems, organisms store essential nutrients, before passing them on to the water, soil or air. Places where essential nutrients can be stored (organisms, water, soil or air) are known as nutrient reservoirs. Nutrients cycle rapidly, through a process known as rapid cycling, passing from producer to consumer to decomposer and back into the environment quickly. Slow cycling is where nutrients are stored and are unavailable to organisms for an extended period of time. Fossil fuels are one such example, incomplete decomposition under high pressures far below the earth. How does both rapid and slow cycling intertwine? The figure to the right explains. The Carbon and Oxygen Cycles Plants consume tones of carbon dioxide (CO2) each year. The overall amount of consumption of CO2 far exceeds its secretion from animals through cellular respiration. A great percentage of carbon dioxide is secreted by forest fires, and by the natural processes of decomposers, in addition to the secretions of human industrial and personal waste. Plants and animals also play key roles in the rapid cycling of oxygen, via the photosynthesis process.

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Trees act as carbon sinks, taking in massive amounts of carbon yearly, and storing it within their trunks until they die, decompose or are exterminated by a forest fire. The rapid reproduction of photosynthetic organisms in the deep ocean also helps to produce a large amount of biomass, which is then consumed by zooplankton, fish, whales and other hetertrophs. Over a long time, the components not broken down by decomposers become part of fossil fuel deposits. The ocean contains approximately 38000 Gt of carbon in the form of dissolved carbon dioxide. A further 11000 Gt of carbon lies on the ocean floor in the form of methane gas. Limestone rock also contains carbon, and as it is weathered small amounts are eroded off into the atmosphere. Humans also have influences on the carbon-air content. For example, during the Industrial Revolution, carbon in the air increased by 30%. The Sulfur Cycle The sulfur cycle works simply. Organisms absorb sulfur into their tissues and organs, and secrete it back out when they die. The sulfurous smell (rotten eggs etc.) is an example of decomposers at work with the sulfur compounds. Some sulfur is taken out of the rapid cycle via bacteria conversion to forms that are layered down as sediment. Sulfur dioxide reacts with water vapor in the atmosphere to form sulfurous acid an sulfuric acid. Acid deposition is the result of these reactions and comes in the form of acid rain, which returns sulfur to the land and oceans. When people burn fossil fuels, sulfur is released into the atmosphere. The Nitrogen Cycle The nitrogen cycle is essential to many organisms. However, many cannot use nitrogen in its pure form and convert it to ammonia (ammonization). Ammonium is also produced during decomposition (ammonification). Denitification is converting the nitrogen or nitrate back into nitrogen gas.

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The Phosphorous Cycle Phosphorous does not cycle through the atmosphere. Instead, it is found within soil and water, and weathering gradually releases it from rocks. Animals obtain it from consuming milk, grain and meat. Scarcity of phosphorous helps to control crops, as it is a requirement to survive. Algae blooms result in a high amount of organic matter in aquatic regions – something that kills off fish and other specifies due to the loss of oxygen. Phosphorous was discovered to be the key link causing the algae blooms, and since that time laundry detergents and dish soaps have had their phosphorous removed to prevent such happenings in future.

Final Notes • • Productivity is the rate at which an ecosystem’s producers capture and store energy within organic compounds over a certain length of time. Stromatolites are rocks that have accumulated sediment minerals over time.

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