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BIOL 103

Walker Readings - Key Terms & Definitions (From Textbook Readings) & Lecture Notes Chapter 39 - Nutrition, Digestion, and Absorption (**See Assigned Reading - Notebook Notes) Term Definition Opportunistic Animals that have a strong preference for one type of food, but can adjust their diet if the need arises Suspension feeders Motile and non-motile aquatic animals, which sift water, filtering out the organic matters Predators Kill live prey Scavengers Eat the remains of dead animals Grazers Herbivores that feed almost constantly on grasses - most chew to facilitate the digestion of plant material Frugivore: adapted to primarily to feed on fruits Fluid feeders Lick or suck fluid from plants or animals and do not need teeth, unless needed to puncture an animal's skin Gastrovascular cavity Digestive cavity (another word for this) Alimentary Canal Canal that food passes along throughout the entirety of the body Digestive system Consists of the alimentary canal (or gastrointestinal tract) and several associated structures Amylase An enzyme that helps to break down carbohydrates, like glucose and other compounds Pharynx Throat Esophagus Upper portion of the alimentary canal, next to the pharynx Peristalsis Rhythmic, spontaneous waves of muscle contraction that being near the mouth and end at the stomach Crop Storage organ in some animals, where food moves from the esophagus to be dilated in the lower esophagus (crop); mainly for birds, so they can regurgitate their food for their young Stomach Saclike organ that evolved as a means of storing and digesting food using the enzyme pepsin (digests proteins - secreted as pepsinogen; activated to pepsin by HCl in the stomach) Proventriculus Glandular portion of the stomach of a bird, which secretes the acid and pepsinogen Gizzard Partially digested and acidic food moves into the gizzard, which is a muscular structure with a rough inner lining capable of grinding food into smaller fragments Chyme A solution that contains water, salts, molecular fragments, and various other small molecules Small intestine A tube that leads form the stomach to the large intestine, and is responsible for the majority of the absorption of nutrients Villi and Microvilli Finger-like projections of the small intestine, with microvilli (small projections on the villi with epithelia cells) - collectively known as the brush border Lacteal Centre of the intestinal villus is occupied by a special type of vessel covered in capillaries that allow the slow of blood vessels in the body Pancreas An elongated gland located behind the stomach that secretes digestive enzymes and bicarbonate ions that neutralize the acidic chyme from the stomach Liver The site of bile production - bile contains substances that help to solubilise fats (include bile salts) Gallbladder Small sac underneath the liver, which stores secreted bile between meals Caecum First portion of the large intestine, which has a small pouch with extends the appendix; cecum of herbivores has microbes that allow to further digest cellulose - more storage Colon Second part of the large intestine, which has three straight segments : ascending, transverse, and descending; final absorption occurs here Defecation Contractions of the rectum and relaxation of associated sphincter muscles expel feces through the final portion of the canal: the anus Transepithelial transport Transport of substances from the lumen to the blood - carbohydrates in particular Trypsin and Chymotrypsin Enzymes secreted in the small intestine that help to break down proteins Aminopeptidase Cleave off one amino acid at a time from the N-terminus (right hand side) Carboxy-peptidase Cleave off one amino acid at a time from the C-terminus (left hand side) Lipase Catalyzes splitting of bonds linking fatty acids to the first and third carbon atoms of glycerol, producing two free fatty acids and a monoglycerides as products Emulsification Process that breaks apart a large lipid droplet into many tiny droplets, which will increase their total surface area and exposure to the lipase action; uses and emulsification agent, which will ensure the droplets do not recombine Chapter 40: Control of Energy Balance, Metabolic Rate, and Body Temperature Term Definition Metabolism All the activities and chemical reactions in an organism's body Metabolic rate The rate at which an organism uses fuel to supply ATP for these reactions Absorptive state Occurs when ingested nutrients enter the blood from the gastrointestinal tract Postabsorptive state Occurs when the gastrointestinal tract is empty of nutrients and the body's own stores must supply energy Chapter 47: Excretory System and Salt and Water Balance Term Definition Ureters Tubes that connect the renal pelvis to the urinary bladder Urethra The tube that eliminates the urine Urinary System The collective system that includes the kidneys, ureters, urinary bladder, and urethra Nephrons Single-cell thick structures in the mammalian kidney; each nephron consists of an initial filtering component (renal corpuscle) and a narrow tubule that extends out from the renal corpuscle that empties into a larger collecting duct Glomerulus A cluster of interconnected, fenestrated capillaries that make up a renal corpuscle (with the Bowman's capsule) Afferent arteriole Arteriole that supplies the glomerulus with blood Bowman's capsule Attached to the glomerulus is a fluid-filled space called the Bowman's space, which is covered by this capsule Proximal convoluted tubule Segment of the tubule that drains the Bowman's capsule Loop of Henle Next portion of the tubule, which is a log loop consisting of a descending limp from the proximal tubule and an ascending lib leading to the next tubular segment (the distal convoluted tubule) Peritubular capillaries Found in the cortex, surround each tubule Vasa Recta Capillaries Found in the medulla, surround each tubule Efferent arteriole Blood leaves the glomerulus through this arteriole Glomerular filtration rate (GFR) Rate at which the filtrate is formed; increased by dilation of the afferent arteriole Filtrate The material that passes through the filter and enters the excretory organ for either further processing or excretion Reabsorption Recapturing useful solutes through active transport pumps or other transport systems; remaining filtrate that is excreted is called urine Chapter 41: Neuroscience I: Cells of the Nervous System Term Definition Sarcolemma An extensible membrane enclosing the contractile substance of a muscle fiber. Sarcoplasmic Reticulum A cellular organelle that provides a muscle fibre's source of the cytosolic calcium involved in muscle contraction Sarcoplasm The cytoplasm of striated muscle cells. Mitochondria Organelle found in eukaryotic cells that supplies most of the cell's ATP Nuclei A membrane enclosed part of a cell that directs the cell activities Chapter 43: Neuroscience III: Sensory Systems Term Definition Sense A system that consists of sensory cells that respond to a specific type of chemical or physical stimulus and send signals to the central nervous system, where the signals are received and interpreted Sensory Transduction Is the process by which incoming stimuli are converted into neural signals Perception Is an awareness of the sensations that are experienced Sensory Receptor Either a neuron or a specialized epithelial cell that recognizes an internal or environmental stimulus and initiates signal transduction by creating graded potentials in the same cell or an adjacent cell Receptor Potential Also known as the membrane potential, where the potential becomes more and more positive as the strength of the stimulus increases; the higher the potential results in more action potential Mechanoreceptors Transduce mechanical energy, like pressure, touch, stretch, movement, and sound Thermoreceptors Respond to cold and heat Nociceptors Also known as pain receptors. Respond to extreme heat, cold, and pressure, and certain molecules, like acids Electromagnetic receptors Detect radiation within a wide range of the electromagnetic spectrum, including visible, ultraviolet, and infrared light, as well as electrical and magnetic fields in some animals Photoreceptors Are electromagnetic receptors that respond to visible light energy Chemoreceptors Respond to specific chemical compounds Chapter 44: The Muscular-Skeletal System and Locomotion Term Definition Locomotion The movement of an animal from place to place Skeleton A structure or structures that serve one or more functions related to support, protection, and locomotion Hydrostatic Skeleton The combination of muscles and water in the body Exoskeleton An external skeleton that surrounds and protects most of the body surface (ex. arthropods) Endoskeleton An internal skeleton that protects the inner organs of the organism Ecdysis Another term for moulting; moulting helps an organism with an exoskeleton to grow through shedding and re-strengthening their body Fast fibres Fibres containing myosin with high ATPase activity Slow fibres Fibres containing myosin with lower ATPase activity Oxidative fibres Fibres that contain numerous mitochondria and have a high capacity for oxidative phosphorylation (split into slow-oxidative - low rates of myosin ATPase activity, and fast-oxidative - high rates of myosin ATPas activity) Myoglobin Oxygen-binging protein, which increases the availability of oxygen in the fibre by providing an intracellular reservoir of oxygen Glycolytic fibres (fast) Few mitochondria, but possess both a high concentration of glycolytic enzymes and large stores of glycogen **Fast-glycolytic fibres Muscle Grouping of cells, called muscle fibres, bound together into fascicles by a succession of connective tissue layers Striated muscle Skeletal muscle; known for its striped pattern Myofibrils Presence of cylindrical bundles in a muscle Sarcomere One unit of repeating pattern of thick and thin filaments along the length of a myofibril Thick filaments Composed of the motor protein myosin Thin filaments Composed of the cytoskeleton protein actin, along with troponin and tropomyosin that play an important role in regulating contraction A band Dark band, where thick filaments are located in the middle of each sarcomere Z line Each sarcomere contains two sets of thin filaments each anchored to a network of proteins along this line; two Z lines define the limits of one sarcomere I band Light band that lies between A bands of two adjacent sarcomeres H zone A narrow, light region in the center of the A band; corresponds to the space between two sets of thin filaments in each sarcomere M line A narrow, dark band in the center of the H zone, which corresponds to proteins that link together the central regions of adjacent thick filaments Cross-bridges Spaces between overlapping thick and thin filaments are bridged by these cross-bridges; these are regions of myosin molecules that extend from the surface of the thick filaments toward the thin filaments Sliding filament mechanism The way in which a muscles fibre shortens as a function of muscle contraction Cross-bridge cycle The sequence of events that occurs between the time when a cross- bridge binds to a thin filament and when it is set to repeat the process Chapter 45: Circulatory Systems Term Definition Blood/Hemolymph An internal body fluid containing dissolved solutes Blood vessels A system of hollow tubes within the body through which blood travels Heart Muscular structure that pump blood through the blood vessels Cardiovascular system Circulatory systems including blood, blood vessels, and a hart Open circulatory system The vessels open into the animal's body cavity, where they mix in the interstitial fluid that surrounds cells Closed circulatory system Blood and interstitial fluid are physically separated by blood vessel walls, and they differ in their components and chemical composition Atrium Component of the heart that is a filling chamber - to colelct blood from the tissues Ventricle Component of the heart that is another filling chamber - to pump blood out of the heart Arteries Blood vessels that carry blood away from the heart to the lungs Veins Deoxygenated blood that is returned to the heart via these types of blood vessels Capillaries Tiny thin-walled vessels that arteries go to arterioles then to capillaries; oxygenated blood diffuses the oxygen across the membrane into cells; capillaries link to venules, which lead into veins, then ventricles Lymphatic system Collects excess fluid and returns it to the blood Chapter 51: Defence Mechanisms of the Body Term Definition Phagocytes Cells capable of phagocytosis, which is when the cell engulfs a material which is destroyed Leukocytes Another term for white blood cells Neutrophils Phagocytes and the most abundant leukocytes; phagocytize and kill bacteria; mediate inflammation Eosinophils Phagocytise parasites; anticipate in allergic responses Monocytes Develop into macrophages Macrophages Phagocytise microbes; mediate inflammation; present antigens to T cells Basophils Enter tissues at site of injury; secrete anticlotting factor: heparin Natural killer cells Attack cancerous and virus-infected cells; also part of specific immunity Dentritic cells Similar to macrophages Mast cells Secrete histamine in inflammatory response Inflammation An innate local response to infection or injury; functions are to destroy of inactive foreign invaders, to clear the infected region of dead cells and other debris, and set the stage for tissue repair Cytokines Family of proteins that function in both nonspecific and specific immune defences and provide a chemical communication network that synchronizes the components of the immune response Interferons Proteins that generally inhibit viral replication inside host cells Complement Proteins Provide another means for extracellular killing or microbes without prior phagocytosis Membrane attack complex (MAC) Five proteins form a multi-unit protein called the MAC, which creates pore-like channels to burst the microbe cell upon embedding itself in the microbial plasma membrane Week 1 - Notes from Walker Lectures: Chapter 38, 39 Two major categories of organisms based on their mode of obtaining nutrients:  Autotrophs: Organisms that harvest light or chemical energy and store it in carbon compounds  Heterotrophs: Organisms must get complex nutrients from the environment; receive nutrition by eating other organisms and are found at higher trophic levels Ways organisms obtain food:  Heterotrophs have many ways of obtaining food - see homework readings  Aquatic animals filter water, and remove organic nutrients  Fungi/ Mold have digestive enzymes that are released over a surface for extracellular digestion to occur: parasites!  Intracellular Digestion - phagocytoses (see Protozoa), where a food particle will be taken into the cell through a food vacuole, and will be broken down using dgestive enzymes  Some paramecium (slipper footed animal) have an oral groove where food goes into organism, then the organism can perform intracellular digestion  Some microbes have created ways to escape phagocytises: pneumonia has a slippery carbohydrate coat, so it is hard to phagocytise - instead, antibodies provide opportunity for the white blood cells to attach to the bacteria  Extracellular digestion (hydra): digested food products are phagocytised directly into the cells that line the gastrovascular - further digested intracellular; wastes are excreted out of the mouth; only one opening in a hydra  See ruminants: (homework notes) Evolution of the Digestive System:  More complex organisms have an alimentary canal with opening at both ends; with several functions of each structure along the canal  Caecum developed during the evolution of plant eating animals; ex. rabbits are well adapted Digestion:  Digestive enzymes convert complex organic molecules into simpler molecules  Digestive enzymes begin in the oral cavity: with teeth and salivary glands (saliva, which contains amylase, helps to break down starch into maltose  The stomach: as food enters the stomach, gastric juices are secreted (like HCl and pepsin)  Pepsin is a protease (member of an enzyme family that is important for the hydrolysis of proteins); helps to convert proteins to polypeptides  How does the stomach not get damaged by HCl and pepsin?  Gastric glands produce pepsin in an inactive form, pepsinogen, which converts to the active pepsin form when combined with HCl  The stomach lining has a viscous mucous layer with a ph of 6, which helps the stomach lining to not be hydrolyzed by pepsin  Parietal cells that produce the HCl don't accumulate the acid; it forms in the stomach after secretion of H+ and Cl- (parietal cells are signaled to produce these ions by the peptide hormone gastrin)  Cells lining the stomach have resistant membranes  Small intestine: the contents of the stomach (acidic chyme) pass onto the small intestine where there is a large number of digestive enzymes produced by the intestinal glands, pancreas, and liver  Intestinal glands: Secretes maltase and proteases (enterokinase, aminopeptidase, dipeptidase)  Pancreas: secretes 5 enzymes:  1) Proteases: carboxylpeptidase, trypsin, chrmotpsin, elastase  2) Pancreatic amylase (converts starch to maltose)  3) Lipase (converts fats to fatty acids + monoglycerides)  4) Nuclease (converts nucleic acids to nucleotides)  5) Sodium bicarbonate  Liver: secretes bile (converts large fat droplets to smaller ones)  Absorption of digested products occurs in the small intestine, which is assisted by the huge surface area of the small intestine, contributed by the villi (contains lacteals, and capillaries) and microvilli, which increase the surface area. Proteases:  Endoproteases: hydrolysis of peptide bonds within a polypeptide (ex. pepsin, trypsin, enterokinase, chymotrypsin, elastase)  Exoproteases: hydrolysis of terminal peptide bonds (ex. aminopeptidase, dipeptidase, carboxypeptidase) Digestion in Insects: Similar to digestion in vertebrates, but no pepsin: adaptations instead  Insects do not have the ability to eat bones, and therefore have no pepsin  Salivary glands: Fruit flies have a special glue  Active proteases eliminated with feces: Insects will secrete proteases to breakdown living or dead animals, which is a form of extracellular digestion **Week 1 Textbook Notes (p.892-894, 899-900)** Week 2 - Notes from Walker Lectures: Chapter 40, 47, 44, 41  After digestion, individual amino acids are absorbed by cells lining the small intestine and then enter the blood Hypotonic/Hypertonic/Isotonic  Isotonic: Solute concentrations are equal inside and out  Hypotonic solution: Solute concentration is lower outside the cell; cells well and may even rupture because water is taken into the cell  hypertonic solution: Solute concentration is higher outside the cell; cells shrink because water exits the cells Saltwater fish vs. Freshwater fish:  Saltwater fish are: hypotonic: in danger of dehydrating with water loss across the gills  Have to drink lots of water; excreted ammonia is diluted with a minimum amount of water (concentrated urine)  Excess salt is transported out of the body by specialized cells in the gills  Freshwater fish: hypertonic: in danger of being "water logged"  Produce large amounts of dilute urine  Specialized gill epithelial cells transport Na+ and Cl- from water into fish's capillaries (concentrate salts)  Relative salt concentrations in various animals various among various animals  Fresh water, Gold fish, Amphibians, and marine fish are all hypotonic  Marine inverts and sharks are relatively isotonic Human Disease associated with excess ammonia (toxic!)  Liver cirrhosis caused by alcoholism, infectious disease (e.x. hepatitis) or fatty liver disease  One of the leading causes of death in the middle years in western countries  One consequence is that the damaged liver cannot efficiently carry out the urea cycle: ammonia build-up can kill you if they have liver disease Ammonia/Urea/Uric Acid  Ammonia: In sharks, the amino acid is deaminated by a deamination enzyme in to a form that can be stored or used for energy, then is secreted as ammonia (mainly occurs in aquatic organisms)  Sharks have evolved to be isotonic to the salt water through the storage of the ammonia  Urea: In humans, toxic ammonia is converts into urea, which is eliminated through excretion  Uric Acid: In birds, reptiles, and insects, ammonia (not using water!, but uses lots of ATP!), is converted into uric acid!  "Guano": known as bird poo - bird excrete uric acid and this is found in droppings with digestive waste; it was important in earlier years as a fertilizer  Ammonia is more toxic, but less energy is needed to produce; urea is in the middle of toxicity and energy cost; uric acid is the least toxic, but requires the most energy to produce Interesting Adaptations 1) Lungfish: lives in shallow waters; during rainfall the lungfish will excrete NH3 as waster, which needs lots of water; when the lake/body of water is relatively dry, the lungfish will secrete waste in the form of urea, which needs less water 2) Salmon (salt water fresh water): When in the ocean, salmon take in water and expel concentrated urine; when in fresh water, then do not take in much water, and expel dilute urine  Gill epithelial cells are able to transport both NA+ and CL- against the concentration gradient (using ATP) 3) Eels (reverse of salmon: fresh water salt water): The American eel is found in fresh and sea waters along the coasts and into Lake Ontario; adapted behaviourally within a matter of days; when balloons were put in eels to see if they live not drinking water in salt water, they died :( Excretory System  To get rid of these nitrogenous wastes, organisms need excretory organs that have the following three functions:  Filtration: acts like a filter to remove water and small solutes from body fluids or blood while leaving behind blood cells, proteins, and other large solutes  Reabsorption: useful material in the filtrate recaptured and returned to the blood; transported across the epithelial cell layer of the tubule  Secretion: may put additional solutes into the filtrate (can aid in the elimination of toxins)  Vertebrates have a kidney (does the filtration to secretion steps above) containing specialized tubules with cells that actively transport ions for salt and water homeostasis and nitrogenous waste elimination; the rest of the urinary system consists of the ureters, urinary bladder, and urethra  The nephron: the function unit of the kidney in higher vertebrates (several million nephrons in each kidney). Nephrons are composed of:  1) Capillary network (used for filtration) : in the renal corpuscle (Bowman's capsule + glomerulus; this forms the filtrate  2) A log tubule that performs secretion and reabsorption  3) A collecting duct that empties into the central cavity of the kidney  For a basic explanation of the kidney, see homework notes below  Water moves very quickly across the nephron membranes through "water" pores, or aquaporins  This discovery explained how water diffuses through the kidney membranes  Aquaporin family can also transport other small molecules (ex. urea)  The protein structure forms loops, which form openings about the same width as the small molecules that will be transported Diseases impacting the Kidney function:  Uric acid in the kidney will lead to kidney stones forming  Diabetes insipidus: no taste in urine  Diabetes I or II: honey/sweet taste in urine Transport in the Kidney  Active transport of NA+ and other substances is needed; active transport is also required in the salt-secreting cells in fish gills  Facilitated diffusion: a channel in the membrane allows transport across the membrane into the cell, or out of the cell (ex. after digestion of carbohydrates, fructose enters the cells lining the small intestine using facilitated diffusion)  Secondary active transport/Co-transport: No energy is required to move one ion with its gradient, which allows another molecule to move against its gradient (ex. Na+ moves with its gradient, which helps glucose to move against its gradient after a meal is eaten) Examples of other pumps 1) P-glycoprotein pump  These are drug efflux transporters which are important for the transport of hydrophobic drugs (helps treat cancer) out of the cell. They have 2 ATP binding sites  Cancer cells increase the gene copy number of p=-glycoprotein; wanting to kill the cell through drugs 2) Bile salt export pump (BSEP)  Helps break up fats in the liver  This ATP-dependent bile salt transport function in the liver  Mutations in this gene can lead to cholestasis characterized by poor fat metabolism, dark urine, severe itching, jaundice, liver failure, and death (some saved with a liver transplant) 3) Cystic fibrosis transmembrane conductance regulator protein (or CFTR permease)  This pump is a chloride transporter found in the lungs, sweat glands and some cells of the digestive tract  2 ATP binding sites, and is an active transporter  Protein bound in the membrane pumps out Cl- ions using ATP  Mutation causes less Cl- to be pumped out of cells, lowers salt concentration Movement and Muscle Control  Plants move using turgor pressure and protists can move using cilia or flagella  Animal cells move using contractile proteins in microfilaments; also move using skeletal muscles that act on the skeleton  Amoeba: moves by attaching actin to a substrate, which catalyzes a reaction for the movement of the cell body  Two major proteins involved in movement:  Actin:
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