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KINE 2011 all notes lecture/textbook.doc
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Department
Kinesiology & Health Science
Course
KINE 2011
Professor
Roy Parteno
Semester
Winter

Description
Page PAGE 4 of NUMPAGES 6 September 11, 2009 KINE 2011 Chapter 1 Homeostasis: A framework for human physiology 1. Body organization 2. Clinical examples 3. Fluids in the body 4. Homeostasis - with examples, mostly negative controls. 5. Data tables on Homeostasis 6. Brief outline on how cells communicate .If you already own Edition #10 of the textbook she will try to point out where it is different than #11 as you will need the book for 2 years time. .She would however recommend that you invest the money to get the Edition #11. .Her pictures that she has taken from the internet are from her MAC computer there may be difficulty with the PC. .She uses clinical examples very often in this course. .Think about how many processes are going on every time you drink a cup of coffee. .It is all done through cell communication. 1. Cells, the fundamental units of life, basic units of a living organism: .Page 2 .How is the body organized ."before exploring ...(Professor changed slides) .There are 200 different cell types. .Muscle, nerve, connective tissue, epithelial cells. Clinical relevance: Stem Cells .A cell than can form any differentiated cell in the body. .A fertilized egg is an example of a stem cell. .They have potential to develop into any type of cell type and can respond to signals and form different tissues. .Identical twins - advantage is the same DNA. .They can transplant any organ into each other. .Research being done now the only way to cure you is to put you on dialysis i.e. for a kidney disease. .There is some research being done where they are trying to put undifferentiated nerve cells into the body to stop Parkinson’s. .If they could take stem cells and put them into the pancreas for people that have diabetes it could cure it without having to take insulin. .There are stem cells that form all of your blood cells. .They can grow stem cells from using embryos. .The hope is stem cells forming organs. Four different tissues: 1. Muscle 2. Epithelial 3. Nerve 4. Connective Surrounded by extracellular matrix Function? - support, transmits signals Major Organ Systems in the Body Circulatory Respiratory Digestive Urinary Musculoskeletal Immune Nervous Endocrine Reproductive Integumentary (See Table 1-1) .Cells are fundamental units of life. Communication: How do cells/tissues/organs communicate? What connects them? Why is this important in Physiology? .Cells exchange nutrients, "factors" and wastes with their surroundings via the "body fluids". Body Fluids - most fluids are water -water accounts for 60% normal body weight -about 42L is water (in 70Kg person) Body Fluid Compartments: Intracellular fluid: 28 L (two thirds) Extracellular fluid: 14 L (one third) : Interstitial fluid (80%) 11L : Plasma (20%) 3L DEF: Intracellular fluid is the fluid inside the cells. .Most of the communication is within the fluids. DEF: Extracellular fluid is the fluid present in blood and the spaces surrounding cells. .The nerves communicate through fibers. .Capillaries: are smaller than a vein and it is about the size of the diameter of a red blood cell. .Most of the exchange takes place through a capillary. .We lose liquids by sweat, blood and urine. .Exchange and communication are key concepts for understanding physiological homeostasis. .Interstitial fluid is the tissue behind the cells. .Cells, the fundamental units of life, exchange nutrients and wastes... (Professor changed slides) .Is a fluid balance important? .Yes .If you run you need to replace the fluids as an example. .Why do I have to understand fluids? .The fluids that carry the electrolytes are critical. Clinical Relevance: Dehydration in dysentery, Dehydration after running in the hot sun Kidney dialysis $1.2 million awarded over wrongful death suit. .Salt restores electrolyte levels. .Hyponatremia associated with over hydration in U.S. Army trainees. http://www.chemistry.wustl.edu/~edudev/LabTutorials/Dialysis/Kidneys.html 2. Homeostasis refers to the dynamic mechanisms that detect and respond to deviations in physiological variables from their "set point" values by initiating effect or responses that restore the variables to the optimal physiological range. .Dynamic is moving. .Set point - examples given using blood pressure it can change. .The levels of sucrose have a set point that you want to get back to. .Example of diabetes it is a disregulation of blood glucose. .You have to have certain ion concentrations. A thought, not on exam! Aristotle: Wrong - the earth is the centre of the universe, the universe is immutable Right - life needs..(Professor changed slides) 2. Homeostasis refers to the dynamic mechanisms that detect and respond to deviations in physiological variables from their "set point" values by initiating effector responses that restore the variables to the optimal physiological range. Scientific DEF: Homeostasis A state of reasonable stable balance between the physiological variables such as blood pressure, body temperature blood borne factors (2, glucose, Na+) Homeostatic Control Mechanisms Hormones Enzymes The nervous system Feedback - negative, positive Set points (not the same as equilibrium which is "non-moving") .Generally it is a negative feedback. .That means the product will stop the reaction. .Positive feedback - it means you are augmenting the response. .Blood glucose levels increase after eating. .Levels return to their set point via homeostasis. .This is an example of dynamic constancy. .Levels change over short periods of time, but remain relatively constant over long periods of time. (Chart shown on screen) Breakfast, lunch, dinner - you eat the most at dinner. .Homeostasis is controlled by feedback. .An example of homeostatic situation is a decrease in environmental temperature. .Room temperature .Heat loss from body .Body temperature .Body's response .Constriction of skin blood vessels .Curling up .Shivering --- involuntary .Heat loss from body .Heat production .Return of body temperature toward original value. (See slide) Integrating Center Specific nerve cells in brain Altered rates of firing (See chart) .The "product" controls the rate of chemical reactions by inhibiting an upstream enzyme (Enzyme A). .This is called negative feedback. .Positive feedback - A series of positive-feedback events promotes the cascade of uterine contractions that promote child birth. .Can the set points be changed? Yes Example: fever, iron, weight? .Fevers stops viruses from growing. .Bacteria need iron to live. .The body will recognize when there are bacteria present and the body will reduce the iron levels. Figure 1-11 Percent increase in total body sodium. Sodium ingested. Sodium excreted. Page 9 Set Point is an important notion Table 1-2 Some Important Generalizations About Homeostatic Control Systems. September 14, 2009 KINE 2011 .Professor has a note that she did not cover reflexes or "processes related to homeostasis" for Chapter 1, pages 1-9, 11-12. .Professor said that she will put the Power Point and the PDF on the website. .She did not cover reflexes because you will take it in detail in the next lecture and she did not feel it was worthwhile going through. .Questions about fevers and shivering - professor advised it is a set point issue. .Normally your temperature is 37.5 while you are infected your body has a new set point it may then be 38.5 or 38.9. .She thinks the text book is trying to say that when you shiver it makes you warm. .Therefore the set point would be 38.5 etc. .This is on page 8 on the text book. So how does the body get messages? How does the pancreas know it should pump out enzymes to the stomach as we eat? .Like all things in life the answer is communication all cells in the body have to communicate. .Cells exchange nutrients, "factors" and wastes with their surroundings via the "body fluids". How (else) do cells/organs communicate? Three categories of signals: .Endocrine: signal reaches target after transport in blood. .Paracrine: signal reaches neighbouring cells via the ISF (interstitial fluid). .Autocrine: signal affects the cell that synthesized the signal (acts on itself). .Pituitary is an endocrine gland. .If you have a cut on your leg how would the bacteria get there? This would be the paracrine system. .If you need to make more of the cell because you are having a reaction there - this is the autocrine system. Types of Chemical Messengers (Figure 1-8) - See chart .A given signal can fit into all 3 categories: .E.g. the steroid hormone cortisol affects the very cells in which it is made, the nearby cells that produce other hormones, and many distant targets, including muscles and liver. Multi-factorial control...Professor changed slides. .The lowest percentages of fluids are actually in the blood. Chapter 2 Chemical composition of the body .Structure/composition of atoms .Concept of molecules .Free radicals - why they are destructive .Bonds - types and strengths .Humans are large collections of tissues and organ systems. .Atoms are made up of subatomic particles: an atomic nucleus with neutrons and protons and a surrounding "cloud" of electrons. Atoms - what do you have to know? Atoms are chemical elements Over 100 elements Named and have names of 1 or 2 letters 24 are essential for the structure and function of the human body. Table 2-1 Essential Chemical Elements in the Body Major Elements: 99.3% of Total atoms Hydrogen - H (63%) Oxygen - O (26%) Carbon - C (9%) Nitrogen - N (1%) Mineral Elements: 0.7% of Total Atoms Calcium - Ca Phosphorus - P Potassium - K Sulfur - S Sodium - Na Chlorine - Cl Magnesium - Mg Table 2-1 Essential Chemical Elements in the Body Trace Elements: Less Than 0.01% of Total Atoms Iron - Fe Iodine - I (Professor changed slides) .You would need to know that the most common element is hydrogen. What do atoms/chemical elements consist of? Table 2-2 Characteristics of Major Subatomic Particles (See chart) .Proton is negatively charged and electrons and positively charged. .So atoms are made of the same particles - what makes them different? .The number of each of the particles Atomic Number - the number of protons Atomic Weight - the number of protons, and neutrons Carbon: 6 neutrons, 6 protons, Hydrogen: 0 neutrons, 1 protons, (Plutonium: 145 neutrons, 94 protons) .Plutonium is used for atomic bombs. Atoms: units of matter that form chemical elements. -C, H, O, N comprise 99% of all atoms in our body -3 subatomic particles make up an atom: protons, neutrons and electrons - Atoms: electrically neutral since protons = electrons. Ions: When atoms are "charged" they are called Ions. .Atoms like to have a balanced electron shell. -can gain or lose electrons in order to balance. .In order to balance its electron it will lose this electron. It will then be 'charged'. Previously, 11 protons, & 11 electrons If it loses this electron it becomes 11 protons & 10 electrons Therefore, 1 +1 charge (written Na+) (See circular diagram) .1 is an unstable state for sodium if it loses its electron it will then become charged +. Free Radicals .Outer electron shells like to be filled - stable atoms. .An atom with an unpaired electron in its outer orbital is a free radical. .Free radicals are very reactive as they "seek" to either loose that unpaired electron or capture another. Why is this important in Physiology? .Oxygen can be free usually it is O2 if it exists as O alone it is a free radical and it is a very reactive molecule and can do damage to your tissue. .It can damage DNA and can damage proteins. .Sunlight can damage the tissues in the skin. .Antioxidants are compounds that can combat free radicals. .Free radicals are very reactive as they "seek" to either lose that unpaired electron or capture another. .Oxygen .The vitamins C and E are antioxidants .Antioxidants neutralize free radicals by donating one of their own electrons, ending the electron - "Stealing". .Scavengers .ROS (reactive oxygen species) - granulocytes. .In some reactions you generate water and there is oxygen in water and this can cause the reaction. .Granulocytes are inside your blood and usually fight bacteria. .They grab electrons that form the cell walls. .Professor said that she takes 1000 mg of vitamin C a day. A few definitions (again): Atoms .Atomic Number - number of protons in an atom (11 is the atomic number for Na) .Atomic Weight - number of protons and neutrons in an atom (23 is the atomic wt of Na - 11 protons, 12 neutrons). .In the neutral, uncharged state, the number of electrons equals the number of protons in an atom. .Outer electrons shells are the most important. Molecules .Two or more atoms bonded together make up a molecule. .Example: a molecule of water contains two hydrogen atoms and one oxygen atom. .H2O. .Pictures in your book that give you the view of how the molecules really are. Bonding/Bonds/Ions .All matter is made of atoms, .Atoms 'bond' together with the same or different atoms to form molecules, and "matter" -Chemical Bonds -Not all bonds formed the same way but they all involve the electrons of atoms. .It is the electrons that are sharing this. .Sodium chloride is an ionic bond. .In water and if you heat them up they become weaker. Types of Bonds Covalent: atoms share electrons (e.g. methane CH4) ionic: opposite charges attract (e.g. Sodium Chloride, NaCl (complete loss or gain of an electrons - no longer neutral, ions are not neutral, they are + or - (positively or negatively) charged (e.g. Cl, Ca+2) Table 2-3 Electrolytes Hydrogen: attraction of positive share in a polar molecule to the negative charge in another polar molecule (e.g. water molecule) van der Waals: attraction between non-polar molecules due to close proximity (e.g. lipid molecules) .Showing bond strength. .Our body breaks bonds with enzymes. .Water is a polar molecule. .Water is held together with hydrogen bonding. Figure 2-1 Covalent Bonds (See chart) In a methane molecule, each of 4 hydrogen atoms is covalently bonded (sharing electrons with) to a carbon atom. Non-polar. Table 2-4 Examples of Nonpolar and Polar Bonds, and Ionized Chemical Groups (See chart) .OH is a hydroxy group. .R is a side group. .SH is sulfhydroxl group .Anything that binds with water is a polar bond. September 16, 2009 105 Bethune College e-mail:[email protected] .Kinesiology clothing will be sold in October. .Tutoring for all Core KINE Courses Group and private sessions check it out!! KINE 2011 Chapter 2 Chemical composition of the body .Structure/composition of atoms .Concept of molecules .Free radicals - why they are destructive .Bonds - types and strengths **.Another section of this course has opened up it is called section C it is a video recorded section. .Those students who are registered in class A & B will have access to the recorded session.**** .Another professor will be teaching the class on Friday as our professor has another commitment. .Question about where section C will be writing exams - they are not sure yet. .Further reviewing bonds - types and strengths. .Different types of bonds have different strengths. .Covalent bonds are the strongest bonds the key word is sharing electrons. .Ionic bonds shared electron has been captured away from one molecule and added to another molecule. .Hydrogen bonds are between molecules they are weaker bonds. .Polar means the electrons in the atom are not shared equally so they become charged. .Non-polar the electrons are shared equally. .More electrons - more negatively charged. .Less electrons - positively charged. .In a methane molecule, each of 4 hydrogen atoms is covalently bonded (sharing electrons....) Professor changed slides. .Hydro carbons are non-polar molecules - olive oil, gasoline are some examples of this. .They do not dissolve most solutes very well. .Polar molecules – are big molecules can have polar and non-polar regions. .Oxygen - is partly negatively charged and negatively charged. .Polar molecules have an uneven distribution of the electron charge. .Ionic bonds - an ion results when a molecule gains or loses one or more electrons. .Ions are mismatched in the number of protons and electrons, and are therefore electrically charged. .Sodium is an atom that can become ionic. .The origin of an ion's proton-electron mismatch is indicated by the sign (plus or minus) and number of signs: Cl- represents a chlorine atom that has gained an electron. .Ca++ represents a calcium atom that has lost two electrons. Table 2-3 Most Frequently Encountered Ionic Forms of Elements (See text) Table 2-4: Examples of non-polar and polar bonds, and ionized chemical groups. ."Like dissolves like" applies here: polar compounds, including water molecules, readily associate with each other, whereas non-polar compounds readily associate with each other, including such compounds in cell membranes. .Hydrophilic, or "water-loving," compounds, e.g. NaCl, dissolve readily in water. .Hydrophobic, or "water-fearing," compounds, e.g. fats, do not dissolve readily in water, but will dissolve readily into non-polar solvents, even cell membranes. .Cells communicate with each other the message has to go from the inside to the outside of the cell membrane. .Cell membranes are made up of a lot of molecules part of it is polar and non- polar. .The non-polar part of the molecule is important. .Example is cholesterol. Hydrogen bonds .In each water molecule, the shared electrons spend more time close to the larger oxygen atom, making that area slightly electronegative compared to the area near the hydrogen atoms. .The dotted lines between water molecules represent the "hydrogen bonds," resulting from the weak electrical attractions. .You can get hydrogen bonding within a molecule. .A lot of biological structures are held by these weak bonds. .Example digesting food in your stomach requires enzymes to break the food down - example eating cereal. .The actual structure you have to separate bonds. .The bonds have to be broken apart before the enzymes can go through. .Hydrogen molecules have a large part in your body. .Covalent bonds are very difficult to close they need enzymes. .In our body we use enzymes. Examples of bonds Covalent: atoms completely share electrons (e.g. methane, CH4) electrically neutral. Ionic: opposite charges attract (e.g. Sodium Chloride, NaCl) complete loss or gain of an electrons - charged. Hydrogen - unequal sharing of electrons - attraction of positive charge in a polar molecule to the negative charge in another polar molecule (e.g. water molecules) van der Waals: unequal sharing of electrons usually between molecules... (professor changed slides) .The shape of a molecule is determined by four different things one of them is the van der Waals. .Solutions-solute/solvent .Concentrations .Molarity, moles .Calculations involved in making solutions that are important in Human Physiology pH - likely on Monday (Friday is beginning of organic molecules in human physiology - Dr. Birot) Solutions .Solutions are substances dissolved in a liquid. -Involves solutes and solvents. Water is the most abundant solvent in our body. .Most of our reactions occur in water. Solutes: substance dissolved in the liquid (solvent). .Solvent: liquid that dissolves the solute. .Solutions: are substances/solutes dissolved in a liquid/solvent. .Water is the most abundant solvent in our body. .Most chemical reactions involve molecules (solutes) dissolved in water - intra- or extra....(Professor changed slides) .To dissolve in water, a solution must be electrically attracted to water molecules (ionized or polar). These molecules are known as hydrophilic (Water loving) .Hydrophobic molecules are water 'fearing' and do not readily dissolve. .NaCl dissolves in water. .Molecules with polar bonds (polar molecules) and/or ionized groups dissole in H2O. .Hydrophobic molecules are water 'fearing and do not readily dissolve (e.g.oil and water) .Some molecules..(Professor changed slides) .Positive sodium ions (Na+) are attracted to negative chloride ions (Cl-) to form ionic bonds. .Amphipathic molecules that have polar and non-polar ends. These molecules form clusters when placed in water. .Important in cell membrane formation. .Important in transport of non-polar molecules in blood, across GI. .Cell membranes mostly made up on amphipathic molecules. .Example is washing your clothes. .A lot of drugs are non-polar they are not soluble in water. .They mix amphipathic molecules with the drug. In a collection of amphipathic molecules, e.g. phospholipids, similar regions will spontaneously arrange themselves with other similar regions. .Here, the non-polar regions associate with each other....(Professor changed slides) Concentration of solutions: .Relationship between the amount of solute and the amount of solvent in a solution. (the amount of solute in a given amount of solvent.) .Can have many different types of units. -weight by vollume: i.e. number of grams/litre .e.g. 9 grams of NaCl dissolved in 1 L of H2O or 9 grams of glucose (C6H12O6) dissolved in 1 L of H2O. But what if we want to know the number of molecules of NaCl or C6H12O6 are present? .You need to know its molarity: i.e. the number of moles/liter. .And from that number can figure out number of molecules. .Moles are per litre. .Moles of the solute per L (of total volume) .The "moles unit" is founded on the fact that molecules have different sizes and different weights. .A mole is reflected in the number of molecules that they are. .Examples: 10 ants and 10 people you have the same number of individuals. .If you weigh them they would weigh differently. If you want to know the molarity it would be the same because you have the same number of molecules. .Atomic Weight: of an atom is number of protons and neutrons in an atom (23 is the atomic wt of Na - 11 protons, 12 neutrons) .Molecular Weight - of a molecule is the sum of the atomic weights (in atomic mass units) of the atoms in the molecule. .Mole: Quantity (number of molecules) of a substance that has the same number of particles s are found in 12,000 grams of carbon-12. This number is named Avogadro's number, and it is 6.022x10 23. .The mass in grams of one mole is equal to the molecular weight in atomic mass units. Page PAGE 1 of NUMPAGES 5 September 18, 2009 KINE 2011 Chapter 2 - starting page 27 Organic molecules Today we will discuss about: -The different classes of organic molecules -The structure of carbohydrates CHO -The structure of lipids -How lipids are synthesized -Protein structure .Professor today is Dr. Birot. What is an organic molecule? .They are molecules containing carbon atoms. .Remember that carbon atoms can combine with each other and with other atoms such as hydrogen, oxygen, nitrogen, and sulfur atoms. .Many molecules can be synthesized from very few chemical elements! .Some of these molecules can be very large!! = Macromolecules / polymers (Thousands of atoms) = depend on the number and nature of monomers involved, as well as on their 3D composition. .There are 4 classes of organic molecules 1) Carbohydrates: Composed of C, H and O atoms. 2) Lipids: C, H 3) Proteins: C, H, O, N (amino acids) 4) Nucleic acids: C, H, O, N (DNA, RNA) Carbohydrates .Only 1% of your body weight, but... central role in chemical reactions providing ENERGY for our cells. .Composed of C, H, O atoms Cn*H2O)n .This general formula=>at the origin of the name "carbo-hydrate" .Water-containing molecules Monosaccharides -smallest subunits. -simple sugars -5 or 6 carbon structures -Include: glucose, fructose, galactose .Glucose is the most abundant 6-C molecule: C6H12O6 "blood sugar" Two representations: 1) Conventional drawing 2) Second representation -Good 3D representation of organic molecules -5 C and 1 O are linked in a ring structure in an essentially flat plane. -H and OH lie above and below the flat ring. -If one H or OH is shifted to the "other side" of the ring, then we have a different molecule! .With one structure a very small change from up to down or down to up it changes the structure. Example: Shift of -OH group from Glucose to Galactose (See diagrams shown) .Combination of monosaccharides to form larger carbohydrates = Polysaccharides 2 monosaccharides = Disaccharides (maltose, lactose, sucrose...) Example: Sucrose, the "table" sugar Glucose + Fructose --Sucrose + Water (See diagrams) .Linking of these monosaccharides= dehydration reaction (production of water) ...Professor changed slides Glucose + Fructose --- Sucrose Glucose + Glucose --- Maltose (digestion of large carbohydrates in the intestinal tract) Glucose + galactose --- Lactose (present in milk) Polysaccharides -made by bonding of 3 or more monosaccharides. -Include: glycogen, cellulose...(Professor changed slides) II. Lipids .Predominantly composed of carbon and hydrogen atoms = hydrocarbons .Atoms are linked by neutral covalent bonds .Lipids are nonpolar, with very low solubility in water. Use: important source of energy, insulation, structure (cellular and organelle membranes) Subcutaneous fat Water temp. 11.8 C After 30 Minutes in water - Central temperature has dropped to 33.7 C in Lean subjects (10% fat) No change in central temperature after 7 Hours in "fat" subjects (30% fat) .This is an illustration of the role of lipids. Table 2-5 Major Categories of Organic Molecules In the Body (See chart) 4 classes Fatty acids - Triglycerides...(professor changed slides) Fatty acids (FA) =chain of carbon and hydrogen atoms with a carboxyl group at one end =Synthesized by the bonding of two-carbon fragments=most common fatty acids have 16-18 carbon atoms. Saturated fatty acid .All of its carbon atoms are linked by single covalent bonds .Fatty acids with one or more double bonds = mono or polyunsaturated fatty acid. Saturated FA .Animal fats (milk, cheese, butter, meat...) .Solid at room temperature due to high melting temperature. Unsaturated FA .Vegetal fats (oils) Liquid at room temperature due to a lower melting temperature. Omega .Indicates the position of the first double bond Example: arachidonic acid is a 20-carbon polyunsaturated FA .Carbon #1 is the carbon from the carboxyl residue. .Its first double bond is on Carbon 14 .It is then a 20-14 = 6 => w6 .Omega 3 or 6 is just indicates the number of double bonds. .Oleic acid (olive oil) has 18 carbons and its first double bond on carbon #9. It is then an omega...#9. .Linoleic cid (w6) and alpha-linolenic acid (w3) are essential fatty acids, not synthesized by our body, so they have to come from our diet. Cis / Trans fatty acids .Most naturally occurring unsaturated FA = cis = both H atoms on the same side of the double bond. (See diagram) .Trans fat have been extensively used in food industry (food storage, consistency, flavor) .But = > implication in Health (cardiovascular diseases) .This is why we try to have less trans fatty foods in our diet when we cook. .Think about changing the way you cook - think about using olive oil. The American Journal of Epidemiology .A high intake of trans fats could increase colon cancer risk. .People who ate the most trans fatty acids were more likely to have pre- cancerous growths or polyps in their colons than those who consumed the least, Another Blow Against Trans Fats in Foods BY Stacey Stowe .Taking on obesity and heart disease Suffolk Country...(Professor changed slides) .Picture of donuts being fried... .Professor said every time that you think about fried foots think about the fat in the arteries (plaque). Triglycerides (TG) = triaglycerols The majority of lipids in humans .Main components of animal fats and vegetal oils .Formed when glycerol (a 3-Carbon alcohol) bonds to 3 FA .The 3 FA do not have to be identical .Dehydration reaction (produces water) Phospholipids Their structure is very similar to TG although there is one major difference = One glycerol molecule is linked to only 2 FA (and note 3), not necessarily identical, and to one phosphate usually having a nitrogen group (N) on it. .The reaction is also a dehydration reaction. .The opposite reaction - hydrolysis - releases....(professor changed slides) Phospholipids are polar (hydrophilic) at the Phosphate end and Non polar (hydrophobic) at the FA end. = Amphiphathic molecules .In water, they will then form clusters with polar ends attracted to water molecules = very important property for the formation of lipid bilayers o plasma and intracellular membranes. (See diagram) Steroids = Different structure for the other 3 sub-classes (FA, TG and PL). Steroids have a skeleton formed of four interconnection carbon rings, with possible few -OH groups attached to this structure. Example: Cholesterol, cortisol etc... professor changed slides) III. Proteins Composed of C, H, O, N and other elements in smaller amounts (sulfur) Macromolecules (thousands of atoms) Often formed by many subunits or monomers these sub-units are amino acids. What is an amino acid? = Subunits of the protein (simplest units) .All amino acids - except one, proline - contain an amino (-NH2) and carboxyl (-COOH) groups bound to the terminal carbon. .Depending on the # of atoms you have different amino acids. .There are 20 amino acids - 20 different side chains (R). The side chain can be polar, non polar, or ionized. (Chart shown) It illustrates the different side chains .Some amino acids cannot be synthesized by the body = 8 essential amino acids. .You then need to get that through your diet. Polypeptides .Two amino acids or more that are linked by peptide bonds (dehydration reaction). .Peptide bonds are covalent but can be broken by hydrolysis (digestion) <50 amino acids => Polypeptide >50 amino acids => Protein (See chart shown) Monosaccharides can bind to the side chain of amino acids = Glycoproteins If you have understood, what identifies a specific amino acid and its function? .The side chain. Structure of proteins .Proteins have multiple levels of structure. =give each protein a unique shape! .This is very important!! Why? ...because the shape of the protein will determine its function = relation structure - function. Primary protein structure .Determined by: 1) number of amino acids 2) nature of the amino acids (20 amino acids) .Depending on what you have in your protein and how they are linked together. For each position on the chain, there are 20 choices If n is the number of amino acids in the chain, then we have 20 n possible combinations! .Example: consider a 3 amino acids chain, 20 3 = 8000 (See diagram of the amino acid chain) .Covalent disulfite bond between two cysteine amino acids. .The primary structure will not stay in that shape. Secondary protein structure Polypeptide = "necklace" composed of beads, each bead being an amino acid. .Amino acids can rotate around bonds giving to the chain some flexibility. .The chain will then adopt a 3D shape = Conformation. (see diagram) .Conformation of the myoglobin How does a protein acquire its conformation? 1) Hydrogen bond 2) Ionic bond 3) Hydrophobic interaction 4) Covalent disulfide bond 5) van der Waals forces (weak) =From strong to weak interactions that all play important roles for the protein conformation. Table 2-6 (See chart) Secondary protein structure alpha helix =Hydrogen bonds between the hydrogen linked to the N atom in a peptide bond and the oxygen from another peptide bond. (See diagram) = This occurs at regular intervals along the chain = >forces the chain to adopt a coiled conformation = alpha helix. (It is a coiled conformation which is called the alpha helix) beta sheet = Hydrogen bonds occur when extended region of the chain run - parallel to each other. =>Straight extended region called beta sheets. (See diagram) .Secondary structure is determined by the primary structure. .Secondary structure brings the notion of protein domains. September 21, 2009 KINE 2011 .Exam is all multiple choice. .There are between 30-50 questions, diagrams items to identify. .Professor advised that the exam will be probably some of chapter 3. .She will not ask you to list the trace elements but she could ask the difference between trace elements and non-trace elements. .Know the common elements and what the trace elements are. Question about whether you need a calculator? .She said you should know how to do long division. Review .In a collection of amphipathic molecules e.g., phospholipids, similar regions will spontaneously arrange themselves with other similar regions. .Here, the non-polar regions associate with each other and the polar regions form hydrogen bonds with the surrounding (polar) water molecules. .Diagram shown Figure 2-6 .There are polar ends that can react with solvents like water which is the main solvent in your body. .Solutions: .Solutions are mixtures of 2 or more elements/molecules blended together. .The solute and solvents of a solution are not held together by covalent bonds (although individual components of a solution can have covalent bonds e.g. coffee with milk and sugar, egg white, chamomile tea. .A protein in a solution - the protein has covalent bonds. .When the sugar is in the coffee that is not a covalent bond. Concentration of Solutions: -Concentration: amount of solute present in a unit volume of the solution (e.g. g/L, mg/L, mg/ml) -Concentration: number of moles of the solute per L (of total volume) (e.g. 1M, 10M, 100mM, 5mM). -The 'Moles unit" is founded on the fact that molecules have different sizes and different weights. .Sodium chloride vs. glucose 5 grams of sodium chloride and 5 grams of glucose are the same weight. 9g glucose - 9g/125ml - 72g/L 9g NaCl - 9g/125ml - 72g/L 9/125ml x 1000 = 72g/L .Change to moles, molarity, molar concentration. .Remember the analogy of ants and humans if there are 10 ants and 10 humans in this flask there are much different weights of each component (ant, human), (say 20g, vs. 700 kg) but the same number of moles (Same number of molecules given that an ant and a human are each "one molecule") Moles per litre - a bit more background first. .You can have molecules of a different size but it is the weight. .Atomic weight - of an atom is number of protons and neutrons in an atom (23 is the atomic wt of Na - 11 protons, 12 neutrons) .Molecular Weight - of molecules is the sum of the atomic weights (in atomic mass units) of the atoms in the molecule. .Mole: Quantity (number of molecules) of a substance that has the same number of particles as are found in 12.000 grams of carbon-12. This number is named Avogadro's number, and it is 6.022 x 10 (23). .One mole of a (ANY) compound contains 6.022 x 10(23) molecules of that compound A CONSTANT. .One mole of a substance weighs its molecular weight, in grams. .A mole of sodium chloride weighs 23 grams. Formula for determining the number of moles in a sample: Number of moles of a substance is = weight of the sample (g) / molecular weight Molarity (of a solution) - # moles/litre 1 mole of a substance = 6 x 10 (23) molecules 1 mole = 6 x 10 (23) molecules = x grams (where x = molecular weight in Daltons (Da) How much does a mole of weight? = x grams .The Periodic Table is where you find what the molecular weights are. .On an exam you will be given the atomic weights of an atom and of a molecule for which she is asking a question. .Hydrogen has 1 proton and 1 electron therefore it is 1. .Fe - which is iron is important in your body. .Iron is found in your blood. How much does a mole of water, H2) weigh? e.g. 1 molecule of H20 H = 1, H2 = 2 O- 16 2 = 16 = 18 Da Preparing/Making Solutions 1 mole of NaCl = 6 x 10 (23) molecules = 58.5 grams .To make a 1 mole/L Na Cl solution (1.0 M NaCl) - 1 mole of NaCl is dissolved in H2O and brought up to a total volume of 1 L. -Sometimes the L is dropped and we would refer to this as 1.0 molar NaCl solution or a 1.0M NaCl solution. .Solutes can add to the volume. .Make a 0.5 mole/L glucose (C6H12O6) solution -0.5 moles of C6H12O6 dissolved H2O and brought up to a volume of 1 L. .C6H12O6 = (6 x 12) + (12 x 1) + (6 x 16) = 180 Da -Therefore: 1 mole of glucose == 180 grams 1 mole/L solution would be 180 g of glucose in 1 L of H2O .Therefore 0.5 mole/L solution = 0.5 x 180 grams = 90 grams/L 0.5M glucose solution = 90 g glucose dissolved in H2O and brought up to 1 L. .A gram molecular weight of glucose 1 GMW = 180 gm of glucose - 1 litre - 1 M solution. .A litre is 1000 ml. . A 100 ml is 1/10th of a litre . 1/10th of 100 grams = 18. .C6H12O6 .You have to add up all the atomic weights of the compound. .This is where 180 comes from. Moles per litre 72/180 = 0.4 - 0.4 moles per L - 0.4M Glucose 72/85.5 = 1.23 - 1.23 moles per L - 1.23M NaCl Solution in flask is 0.4M glucose, 1.23M NaCl. .There are at least 3 questions on the exam that will require this type of calculation. Solutions .Concept of concentration e.g. g/L and M/L or molarity of the solution. .Molecular weight, how to calculate it for a molecule given its formula. .Concept that one mole of a substance/molecule has the same number of molecules as all other substances/molecules, BUT the weight of one mole of a molecule/substance depends on its chemical composition (neutrons, protons, electrons) .Molar, Molarity, Molecular Weight, moles per litre. .If I gave you 2 moles of sodium chloride - how many molecules would you have? .12 x 10 (23). .Professor advised she will not ask about significant figures. pH Neutrality is rare .It is the measure of the acidity or the alkalinity of a solution. Concept that solutions have acidity, Concept that acidity is determined by the Concentration of H = in a solution And remember Human bodies are mostly water, thus mostly in solution So why is pH important for human physiology? .In order for our chemical reactions to work the pH of the solution is very important. .Enzymatic reactions do not work with extreme solutions. .Our systems are buffered so that we can keep the pH's around 6-7.5. The pH value indicates the acidity of a solution. .The concentration of free hydrogen ions in a solution is the primary determinant of that solution's acidity: pH = -log(H=) .Remember that the representation "(x)" is a quick way to state "the chemical concentration of a solute x" Strong vs. Weak Acids .Strong acids completely dissociate in H2O HCl ---- H= Cl- .Weak acids partially dissociate in H2O Lactic acid (HLa) ----HLa --- H+ La- 95% 5% Which do you think are most prevalent in humans? Strong or weak? .Answer is weak acids. .Most of the acids in our body are weak acids except in our stomach. .pH scale = 0-14 .pH = -log 10 (H+) Increased (H+) pH range for life is pH 6.8 to pH 7.8. September 25, 2009 KINE 2011 .Midterm is on Oct 2/09 on Friday - there are 2 lecture halls. .Look on WebCT to find out which lecture hall you will go to in order to write the exam. .Section C is being divided between the 8:30 exam and the 9:30 exam. .When you come you will wait until the students leave the room before you enter. .The exam time is 50 minutes time it will be a scanatron multiple choice, there will also be a diagram. .The textbook is a required text. .She has tried to cover everything that is in the text. .It would be rare to ask something that she had not talked about understand all of the lecture material. .Example if you had a pH of 2 would it be compatible with 1? .Bring your pencils and erasers and your student #'s to identify you. Chapter 1-9, 11-12 Chapter 2 - complete chapter Chapter 3 - at least up to cell organelles .Every large molecule in your body is composed of subunits. .Amino acids are subunits of protein. .Monosaccharides are subunits of sugar. Diagram shown on screen .One difference between DNA and RNA? .In the case of DNA it is called deoxy - no oxygen. .It is a ribose sugar it has 5 rings .The structure of DNA is base, sugar and phosphate. .The bond shown is covalent. .The phosphate is covalently joined to the sugar base. .Another difference between DNA and RNA are the type of bases. .In DNA the bases are adenine, guanine, and thymine. .DNA is double stranded. In RNA the bases are adenine, guanine and uracil. .RNA strands are usually single. The sequence of bases in DNA (and in RNA) is held together by phosphate-sugar backbone. Which bases are Purines? Pyrimidines? .Adenine is a purine it is a 2 ringed structure. Purines - A, G (energy transfer molecules) Pyrimidines - C, T Guanine (DNA and RNA) Cytosine - (DNA and RNA) Uracil (RNA only) What is a nucleotide? .Phosphate sugar base. Figure 2-25 (See diagram) Hydrogen bonds between complementary bases hold together the DNA double helix. .The strands are anti-parallel. What holds the strands together? .They are hydrogen bonded weaker bond that can be broken apart easily. .There is actually some stacking between the thymine and cytosine - this area of the molecules is non-polar (hydrophobic) there are some van der Waals forces in this. .The stronger interaction is between G-C. What are complementary bases? .Bases that bind together. Watson and Crick and Franklin Discovered structure of DNA This was done by x-ray crystallography A:T G:C .Science is generally done by teams of people. Figure 2-25 Figure 2-24 diagrams shown .The two strands are kept the same distance apart. .Know that G and C bind to each other. .Example A and T bind together. Table 2-7 Comparison of DNA and RNA composition (See chart) .ATP serves as the energy currency of the cell since the hydrolysis that removes one phosphate group is accompanied by a discrete and controllable energy release. Figure 2-26 (See diagram) ATP + H2O >>>>ADP + P1 + H+ 7 kcal/mol .This is done by an enzyme it is therefore controlled. Chapter 3 - cells Cell Structure and "PROTEINS" Section a (text) Cell organelles pp 43-54 (covered) Nucleic acid structure pp 36-39 Section B text ....(professor changed slides) .Structure determines function. That which alters structure alters function. .Cells: Membranes - internal and external partitions nucleus - genomic DNA RNA - tx, ribosomes - protein synthesis endoplasmic reticulum - protein...(Professor changed slides). .Genes to protein (this will take at least 5 lectures as per professor) Figure 3-2 .This scale is a logarithmic scale. .It is a base 10 scale. .A cell is about 10 microns. .Your red blood cells are smaller they are about 5 microns and that allows them to get through capillaries. .Most cells are between 8-10 microns. .Your neurons can be very large. .On average a cell is 10 microns. .1 micron is about the size of bacteria. .Most cells are spheres. .The most energy efficient shape is round. .Most cells when they are free are round. .Cells when they are functioning in a tissue can take on different shapes. .The lining of your gut are epithelial cells they are stuck to each other. .Most cells in membrane structure are cuboidal. .Most cells are two dimensional. Figure 3-3 Diagram Electron Micrograph of organelles in a hepatocyte (liver cell). Nucleus - it has a very long membrane and that membrane has 2 layers. (bilayered membrane) Mitochondria enzymes need energy and are broken down in the mitochondria. Rough endoplasmic reticulum - they are ribosomes. Golgi - named after a person called Golgi. .It functions in modifying proteins to be secreted by the cell. .Lysosomes are sites that break down proteins. .pH range for life 6-8 --- 7.8 .Lysosomes are out of that range. .When lysosomes break open that cell is going to die. Figure 3-4 Diagram .Structural & functional unit .Eukaryotic cells have membrane bound organelles .Cytoplasm is everything outside of the nucleus. .Cytosol is everything outside the organelles. .Nucleoli are dark cells. .Parts of ribosomes are assembled there. Eukaryotic cells have a nucleus. .Bacteria do not have a nucleus. .Membranes are protecting everything inside from everything outside. .There are membranes around the organelles. .Viruses do a lot of work in the cytoplasm. Table 3-1 Functions of Cell Membranes 1. Regulate the passage of substances into and out of cells and between cell organelles and cytosol. 2. Detect chemical messengers arriving at the cell surface. 3. Link adjacent cells together by membrane junctions. 4. Anchor cells to the extracellular matrix. (extracellular means outside the cells) Figure 3-6 Diagram Red blood cell .This is a membrane of a cell. .A membrane is 2 molecules thick a phosphate and a lipid. (phosphobilipid bilayer) .This is an amphipathic molecule. .Sugars are often outside covering the membranes. Proteins in membranes -Integral - cannot be extracted without disrupting membrane...(Professor changed slides) September 30, 2009 KINE 2011 Mid-Term Exam Schedule Section C only, you may trade times (not rooms) if you have a course conflict. Examination rooms are CSE A and CHL L. Please make sure you know where you are supposed to be. Exam is multiple choice using "scanatron",please bring pencils, erasers, you can use calculators and of course, student ID. 8:30 - 9:30 All of Section A, half of Section C CSE A Section A: Abbaszadegan M to Kuban M, inclusive Section C: Aiyegbus J to Fernandes B, inclusive CLH L Section A: Kufakwedu M to Zlobine I, inclusive Section C: Fernandez A to Marcoux D, inclusive 9:30 - 10:30 All of Section B, half of Section C CSE A Section B: Abdul-Rahman S to Manavipour A, inclusive Section C: McDonald A to Ryu D, inclusive CLH-L Section B: Manca M to Ziobrowski M, inclusive Section C: Sauer K to Yu A, inclusive .Professor said to look on WebCT as there might be a room change. Cell Structure and "Proteins" Section A (text) Cell organelles - Chapter 3, pp 43-54 (covered) Nucleic acid structure - Chapter 2, pp 36-39 Section B (text) Gene expression: transcription and translation - Chapter 3, pp 55-63 Promoter activities Chapter 3, pp 60-63 Modification and turnover of proteins - Chapter 3, pp 63-65 Section C (in text) Protein building - Chapter 3, pp 65-71 .Molarity is very important to know! Figure 3-3 Electron Micrograph of organelles of liver cell Nucleus .Almost all cells have a single nucleus (rbc, liver, megakaryocytes) Function: storage and transmission of genetic information take part in cell's protein manufacturing. Figure 3-12 Endoplasmic reticulum .The name reticulum came about because people would look and see all these networks. .They know that some are rough and some are smooth those two structures have different functions. Rough Endoplasmic Reticulum .Rough parts are ribosomes that are stuck to it. .This is where proteins are made that will be secreted .They pass into the endoplasmic reticulum. .The rough E.R. is where proteins are made. Smooth Endoplasmic Reticulum .It has two different functions: one is synthesis contains enzymes for fatty acid and steroid synthesis. .Also stores and releases calcium, which controls various cell activities. Ribosomes .Protein factories, .Large particles - 20 nm diameter, 70-80 proteins plus RNA Typical cell has 10 million ribosomes Free vs. membrane (Endoplasmic reticulum) bound ribosomes. .Membrane ribosomes are part of the rough endoplasmic reticulum. Figure 3-21 Picture of Ribosome - this will be covered on Monday. Figure 3-13 Golgi Apparatus Structure .They are flattened membrane structures. .It is connected to the rough endoplasmic reticulum. Function: concentrates, modifies and sorts proteins arriving from the rough endoplasmic reticulum prior to their distribution, by way of the Golgi vesicles, to other organelles or to secretion from the cell. .Sugars can be added in the Golgi, proteins etc. .Transport vesicle delivers proteins to other organelles (contribute to organelle synthesis) .Vesicle fuses to membrane. .Secretory vesicle delivers proteins to plasma membrane for section. .Secretion (exocytosis) (e.g. a hormone like insulin) .Endings of nerve cells, secretory vesicles. .Released into interstitial fluid, Where they can modify the activity of nearby cells. Endocrine, Autocrine, Paracrine (know these definitions) .Endocrine always means the chemical goes to the bloodstream. .Not all chemical messengers can be transmitted in all three ways. .Insulin is secreted by the beta islet cells of the pancreas. Figure 3-14 Mitochondria (plural) Mitochondrion (single) .Powerhouses of the cell. Mitochondrion Structure: Rod - or oval-shaped body surrounded by two membranes. Inner membrane folds into matrix of the mitochondrion, forming cristae. Function: Major site of ATP production, O2 utilization, and CO2 formation. Contains enzymes active in Krebs cycle and oxidative phosphorylation. .Structure always has something to do with function. .The more active a cell has the more mitochondria it has. .Muscle cells are more active. .Energy is made in the mitochondria in the form of ATP. .As many as 1000 in active cells. .All your mitochondria come from your mother. Mitochondria/Mitochondrion .Mitochondria provides 95% of cell energy needs (ATP) (mitochondria) in cell is proportional to the ENERGY requirements of the cell. .The other 5% is from Glycolysis. .Article - A neurological awakening .There are a lot of mitochondria diseases. .Mitochondria have DNA and they make proteins. .Patient was being treated by depression and they discovered that he had a mitochondria disease which led to the depression. .This is a genetic disease and it was discovered by researchers. .Mitochondria contain proteins called CYTOCHROMES-critical for ATP production Cytochrome has a red pigment due to the presence of iron containing Heme. .Mitochondria phosphorylation only require oxygen. .In iron deficient diet: Decreased cytochrome synthesis>>decreased endurance (also decreased hemoglobin synthesis>>anemia) Lysosome (oval/sphere, not a tube, not membranous sac) .Debris could be bacteria, and organelles or denatured proteins. .Lysosome (digestive enzymes inside lysosome degrade debris) Peroxisome - works with the lysosome in the degration of intracellular debris. .The lysosome and peroxisome digest the material that could harm the cell or are waste products - digestive factories - harbour harmful materials (e.g. H2O2) .Example if you pour hydrogen peroxide on a wound it is degrading the protein. Cytoskeleton .Inside the cell, as well as organelles there are protein filaments that give "structure" to the cell. .Collectively called the cytoskeleton. 1. maintain cell structure 2. produce cell movement (e.g. contraction), 3. provide structure for cell division (chromosome separation) 4. provide attachment surfaces for plasma membrane, enzymes and receptors. Cytoskeleton - 3 types of filaments Microfilament - Actin - small diameter, rapid turnover, e.g. structural. Intermediate filament - Several proteins intermediate diameter, low turnover, multi-protein complex, e.g. desosomes Microtubule - Tubulin - Large diameter, rapid turnover, e.g. cell division. October 9, 2009 KINE 2011 To see your exam booklets, the next TA sessions will be held in the professors office area - 124 Farquharson Bldg (Monday 19th Oct and WED 12:30-3:30) and thereafter Or by appointment! CELL STRUCTURE AND PROTEINS CONT'D Section C Regulation of protein binding - Chapter 3, pp 66-71 Protein binding sites Binding site - region of the protein where ligand binds Ligand: any molecule that is bound to the surface of a protein by one of (the following forces): 1. electrical attraction between (oppositely charged) ionic or polarized groups (on both the ligand and the receptor/protein molecules) 2. Weaker attractions due to van der Waals forces between the (non polar regions on) two molecules Non covalent bonds - therefore reversible Ligand-protein BINDING IS REVERSIBLE .If you have a protein and another protein there is going to be a reaction with each other. .A lot of the proteins in your body are not working they are just sitting there and waiting for a signal that tells them to work. .The interaction changes either the ligand or the receptor. .Professor said that when the book uses the term electrical - it is ionic. Protein binding is affected by: specificity, affinity, competition, saturation "Regulation of binding site characteristics" Proteins are associated with practically everything that occurs in a cell. How do you control protein activity? 1) Change the protein shape (alters binding of ligands) 2) Regulate protein synthesis and degradation. Figure 3-26 (See diagram) Shape and charge work together in matching up ligands with their receptors. .It could be a polar interaction or an ionic interaction. REGULATION OF PROTEIN BINDING - Figure 3-27 (See diagram) The Shape and charge distribution of a binding protein determine which ligands it will bind. Note: the binding sites do not need to be adjacent along the polypeptide chain. The amino-acid sequence of a protein determines both shape and the distribution charge. .This was all discovered through genetic engineering. Figure 3-28 (See diagram) Protein X binds a wider diversity of ligands than does Protein Y. Protein Y has greater ligand - specificity than Protein X. .Shape determines the charge and the shape. .In your body which is more useful? .In some cases you only want the ligand to bind with the one receptor. .This is not always the case some ligands bind with other receptors. .In an enzymatic reaction you want specificity. .It is a balance. Affinity - the strength of the ligand-protein binding (a property of the binding site) The strength of the interaction/of the binding .Usually when a ligand and a receptor come together - how long they stay is a measure of the interaction - we are talking nanoseconds and microseconds. .The length of time they stay is a measure of the strength of the interaction. .Next slide shows affinity Protein 1 Protein 2 Protein 3 high affinity intermediate low affinity binding site binding site binding site Saturation - a measure of the fraction of total binding sites that are occupied at any given time. -depends on concentration of the unbound ligand, and affinity of the binding site for the ligand REFERS TO THE BINDING SITES - THE SATURATION OF THE BINDING SITES Saturation - (fraction bound) The concept of equilibrium bound - unbound - bound. .So a single binding site is either bound or unbound by ligand. The fraction....(Professor changed slides) Figure 3-30 (See diagram) Saturation occurs when ligands become so abundant that every binding site is occupied. .The point of reference in these slides are the receptors. When two proteins can bind the same ligand, Competition saturation occurs more readily for the protein that has a higher affinity (Protein Y, here for the ligand) Figure 3-31 (See diagram) Which receptor has a higher affinity for the ligand? .It is the blue coloured diagram. How do you control protein activity? 1) Change the protein shape (alters binding of ligands) What determines protein's shape? (remember back to the 4 levels of protein shape Chapter 2) And remember that some AA are charged...(professor changed slides) .There are two mechanisms that CAN selectively modify protein shape (only in some proteins) Allosteric and Covalent modulation Allosteric this is reversible. Figure 3-32 (See diagrams) .An allosteric modulator forms a non-covalent bond with the protein. .A covalent modulator forms a covalent bond with the protein. What is ATP? - Energy transfer not energy storage. .A kinase adds on a phosphate. Figure 3-37 (See diagram) Any given enzyme can have a diversity of allosteric and/or covalent modulation sites. .It is like a storage they are there and waiting. Enzymes pp 71-77 .You have studied the synthesis, degradation and regulation of proteins .Here the focus is function of proteins .Enzymes facilitate chemical reactions .Enzymes are (mostly) proteins. Enzymes .In humans very few reactions/chemical reactions/metabolism take place without enzymes .BUT in theory, every chemical reaction is reversible .Some enzymatic (chemical) reactions are reversible. .Both forward and backward reactions are catalyzed by same enzyme. Law of mass action: direction of the reaction is from side of equation where concentration is higher to side where concentration is lower. Page PAGE 1 of NUMPAGES 4 October 19, 2009 KINE 2011 Cell Structure, Proteins and Metabolism, Chapter 3 The week of Oct 19-23, 2009 Section D Enzymes & Chem Energy -some covered before study week Chapter 3 pp 71-77 Section E - Metabolism pathways: Glycolysis Kreb's cycle Chapter 3, pp 78-92 Oxidative phosphorylation YOU ARE NOT RESPONSIBLE FOR EVERYTHING IN THE TEXT, AS WILL BE EXPLAINED IN CLASS Energy metabolism Course notes only (The text goes into more details than necessary for a student of Human Physio Kine 2011 - but it is interesting and is helpful overall information.) TA Session is in 124 FARQ 12:30-3:30 Drop in. .Professor is willing to meet with students who are doing under 80% in this class you can e-mail her to meet with her. Enzymes pp 71-77 .You have studied the synthesis, degradation and regulation of proteins .Here the focus is function of proteins .Enzymes facilitate chemical reactions. .Enzymes are (mostly) proteins. .In humans very few reactions/chemical reactions/metabolism take place without enzymes. .BUT in theory, every chemical reaction is reversible. Reactants --------forward Products --------reverse--- .Some enzymatic (chemical) reactions are reversible. .Both forward & backward reactions are catalyzed by same enzyme. .Law of mass action: direction of reaction is from side of equation where concentration is higher to side where concentration is lower. For the reversible reaction: A + B -------- C + D C + D CO2 + H20 .Professor is giving an example of opening up a can of coke the bubbles are CO2. .In your mouth you have the carbonic anhydrase which breaks it down. By itself, the reaction takes 100 seconds/CO2 molecule. .In the presence of the enzyme, Carbonic anhydrase, takes 1 second/100,000 C02, molecule. .Substrates fit into active sites. .Enzyme-substrate complex formed. .Reaction occurs. .Products dissociate .Enzyme is unaltered .Most enzyme names end with "-ase" .Classes of enzymes named according to activity .Such as phosphatases that remove, or kinases that add phosphate groups. .Name may specify substrate of enzyme & activity, such as lactate dehydrogenase. (These words are important in gene regulation as per professor) .Sometimes enzymes need help. Cofactors .Often trace metals (eg Zn, Fe, Cu, Mg) Bind to enzyme, cause change in structure (conformation) of enzyme. Coenzymes - organic cofactors - they participate in the reaction (get added to the substrate for example) - transfer/add small molecules (H, CH3, acetyl) But can be released from the substrate ("reverse reaction") and be reused. Derived from vitamins - NAD + and FAD derived from B vitamins, niacin and riboflavin. R-2H + coenzyme ________> R + coenzyme -2H. Table 3-7 Characteristics of Enzymes 1. An enzyme undergoes no net chemical change as a consequence of the reaction it catalyzes. 2. The binding of substrate to an enzyme's active site has all the characteristics - chemical specificity, affinity, competition.... (Professor changed slides) Some Characteristics of Enzymes - (Please also study Table 3-7 which summarizes) .Enzymes have optimal temperature & ph ranges -Typically near normal physiological values -Because (3-D) structure is affected outside range. (See graphs) .Professor said the optimal temperature in your body is 37.5. .Pepsin resides in the stomach. .Salivary amylase is made in your mouth. Figure 3-34 p 75, Regulation of Enzyme-Medicated Reactions Rate depends on substrate conc. and concentration of enzyme. (See graph) .Saturation of enzymes occurs when substrates become so abundant that all enzymes are participating fully. .Professor said that eventually the enzyme will die. Enzyme activity .Increasing the availability of enzymes results in an increased rate of reaction. (See graph) .If you have less enzyme the rate is slower. .If you have more enzyme the rate is faster. .Enzymes are (mostly) proteins, therefore to increase the enzyme concentration either the synthesis of enzyme has to increase or degradation, decrease. .An allosteric or covalent modulator that increases an enzyme's affinity for its substrates will increase the rate of product formation. (See graph Figure 3-36) Three things on these last three slides - Changed substrate concentration Changed enzyme concentration Changed enzyme activity by allosteric or covalent modulation. Figure 3-37 (See graph) Any given enzyme can have a diversity of allosteric and/or covalent modulation sites. .Metabolism - coordinated process of chemical change. .Breaking bonds and creating new bonds. .Synthesis and breakdown of organic molecules required for cell structure and function in our body. Anabolism (building up), and catabolism (breaking down) .Professor advised most of these are covalent bonds. .Vegetarians require a lot of amino acids to be able to build all the muscle that you need. Coenzymes Help enzymes achieve their full activity. Note: co-enzymes actually participate in the reactions. BUT Coenzymes can be recycled and a single coenzyme can be used over and over again. Figure 3-40 (See graph) .This is catabolism - breaking down fuels provides chemical energy to rebuild ATP supplies. Anabolism: creating bonds, uses energy (ATP) Catabolism: breaking bonds, releases energy (may be in the form of ATP) Three metabolic pathways: Glycolysis - occurs in Cytosol in which carbohydrates are broken down, mitochondria in Krebs cycle, Coenzyme - 2H Metabolism: How does the food you eat turn into energy "Enzyme play a huge role -physiological reactions that together promote the homeostatic state and, of course, (Professor changed slides) ATP .The molecule that receives (does not store it) the transfers of the energy from the metabolism of food is ATP. (If we are in a food deficit, use our body's stores) Figure 2-26, page 39 (See diagram) ATP - Adenosine Tri Phosphate High energy bond: between P and O in the terminal phosphate. ATP ------>ADP + P1 Energy (professor changed slides) Food Carbohydrates Fats Proteins Metabolism: how does the food you eat turn into energy What are the (in general) rules? Glycolysis - only Carbohydrates undergo glycolysis, -takes place in the cytosol -can occur with or without oxygen (O2) (in the presence or absence of O2) Krebs cycle and Oxidative Phosphorylation utilize all food groups, (Carbohydrates, Fats, Proteins) -take place in mitochondria -require oxygen (02) 90 seconds All generate energy -....professor changed slides. Glycolysis .Catabolizes CHO (primarily glucose) .10 enzyme reactions (anaerobic) which convert glucose ring 6 carbon ring) to 2, 3 carbon pyruvate molecules. .Net gain of 2 ATP, 4H+ (2H+ transferred to 2 co-enz, NAD+, 2H+ released as ions) .No reaction utilizes Oxygen O2) (See Fig 3-41) .The first few steps of glycolysis, glucose is converted into fructose, 1, 6- diphosphate. .Even though....professor changed slides Glycolysis produces a net gain of 2 molecules of ATP and 4H+...professor changed slides... Figure 3-41 Glycolysis: A net gain of 2 molecules of ATP and 4 atoms of hydrogen. Table 3-8 Characteristics of Glycolysis (See slide) Page PAGE 1 of NUMPAGES 6 October 21, 2009 KINE 2011 Figure 3-21 (this is an older slide) apparently the numbers were not in the correct order Elongation Step: 1. tRNAs bind to site 1 & 2 2. tRNA at site 1 exits after donating AA. Figure 3-40 (See slide) This is catabolism Breaking down fuels provides chemical energy to rebuild ATP supplies. Anabolism: creating bonds, uses energy (ATP) Catabolism: breaking bonds, releases energy (may be in the form of ATP) .We are following the sugar molecule. .ATP is transferring energy to the site. .The Kreb's cycle and Oxidatitive phosphorylation requires oxygen. .CO2 comes from your mitochondria. .1 molecule of glucose generates 2 pyruvates of lactate. What's in a name? Krebs acid cycle Citric Acid cycle Tricarboxylic acid cycle (Second of three pathways involved in fuel catabolism and ATP production) Krebs: utilizes the molecular fragments formed during CHO, protein and fat breakdown and it produces CO2, H and some ATP. Enzymes for Krebs are in the inner mitochondrial compartment, the matrix. Entering material/molecule for Krebs: Need an acetyl group from pyruvate (glycolysis) or from the breakdown of fatty acids or from SOME amino acids. .The acetyl group reacts with Coenzyme A, to produce acetyl COA .The primary molecule entering at the beginning of Krebs is Acetyl CoA. .The purpose of these cycles is to generate energy from the food that you eat. The acetyl group reacts with Coenzyme A, to produce acetyl CoA....professor changed slides Figure 3-43 (See slide) How does pyruvate enter Krebs? As acetyl CoA. CH3 NAD+ NADH + H+ CH3 | | C=O + CoA - SH------------------C=O + CO2 | | COOH s- CoA pyruvic acid Acetyl coenzyme A Each transition of pyruvate... Page 46 Picture of pyruvate Mitochondria: Rod or oval shaped body surrounded by two membranes. Inner membrane folds into matrix of the mitochondrion, forming cristae. Function: Major site of ATP production, O2 utilization, and Co2 formation. Contains enzymes active in Krebs cycle and oxidative phosphorylation. .These reactions are to generate energy. .The energy is captured when ADP converts to ATP. .The energy used to move your arm is ATP. Krebs cycle Figure 3-44 (See diagram) .8 enzyme pathway .In aerobic conditions, 2 spins of the Krebs cycle occur for each glucose that enters glycolysis. BUT FORGET NOT!!! .FATS AND PROTEIN METABOLITES ALSO CONVERTED TO ACETYL-COA. .NADHs & FADHs are the only substrate of phosphorylation. .They will give up their hydrogen later to become oxidized. .It is a cycle it goes around and regenerates its starting material. .For every cycle it generates 1 ATP. Summary of Krebs reactions Acetyl-CoA + 3 NAD+ FAD + GDP + Pi + 2H2O >2CO2 + CoA + 3 NADH+H + FADH2 + GTP (note GTP converted directly to ATP) The coenzymes NAD+ and FAD pick up electrons (become 'reduced') at steps 3, 4, 6 and 8. Hydrogen state in NADH Diagram of an Hydrogen atom (electron is a "cloud" - don't know where it is) Table 3-9 Characteristics of the Krebs Cycle Page 52 Oxidative Phosphorylation Third pathway: Generates the most ATP per input molecule (quantitatively the most important mechanism by which energy derived from fuel molecules can be transferred to ATP). The energy transferred to ATP is derived from the energy released when H ions (protons) from NADH + H+, and FADH2 combine with molecular O2 to form H2O The H comes from the NADH + H+ and FADH2 coenzymes generated by Krebs, (and by metabolism of fatty acids) 1/2O2 + NADH + H+ ----> H2O + NAD+ Energy Enzymes that do the reactions 1. Those that transfer H+ to O - Cytochromes - form the electron transport chain 2. Those that couple the energy released by 1. to synthesis of ATP. Enzymes for the oxidative phosphorylation are located in the Inner mitochondrial membrane. Figure 3-45 (See diagram) .From Input#1, 3 ATPS are formed. .From Input #2, 2 ATPS are formed. .Chemiosmotic hypothesis. .It generates ATP from the electrons gathered. .Energy has to be captured away. .By making water energy is released - the hydrogen’s once they reach a high enough concentration - oxidative phosphorylation takes place and you generate energy. Chemiosmotic hypothesis As e-(electrons) are transferred from one cytochrome to another along the e- transport chain the E (energy) released is used to move H+ (protons) from the matrix into the intermembrane space producing potential E (a H ion gradient) at three points on the chain channels form H ions flow back to matrix, and in the process transfer E to form of ATP. 1961 - accepted in late 60s Nobel Prize for Mitchel in 1978. Table 3-10 Characteristics of Oxidative Phosphorylation (See slide) Figure 3-46 Page 85 of your textbook (See slide) .This 100% efficiency, no FADH2 in glycolysis, usually number given is 36, and sometimes 34. ***(THIS WAS POSTED ON SCREEN BEFORE THE CLASS STARTED)*** Other fuel sources: Glucose Glucose - only one of many Other CHO (carbohydrates) Triglycerides: glycerol and fatty acids Lipids (fatty acids) Proteins (amino acids) Acetyl CoA is the key: All the "potential" energy in these molecules can only be harnessed if they enter the Krebs Cycle, and generate NADH/FADH2 To enter Krebs must be converted in to acetyl CoA. Page PAGE 4 of NUMPAGES 4 October 23, 2009 KINE 2011 Cell Structure, Proteins and Metabolism, Chapter 3 The week of Oct 19-23, 2009 Section E - Metabolic pathways: Glycolysis Krebs Cycle Chapter 3, pp 78-92 Oxidative phosphorylation Up to p84 - we have covered it in class P85 covered it P86-91, text and notes- Nitrogen balance (p90) not covered Fig 3-49 no detail required - notes are better Fig 3-50, covered but not in detail, 3-51 not covered Fig 3-53, covered but not in detail Essential Nutrients - not covered Figure 3-46 (See diagram) .The purpose is to generate ATP. .This 100% efficiency, no FADH2 in glycolysis, usually number given is 36, and sometimes 34. .38 is optimal for generating ATP's .In order to enter the Krebs A+B for glycolysis is a carbohydrate + glucose C+D is the glycolysis pyruvate. .Acetyl coenzyme A is the substrate. .Acetyl CoA is utilized in the matrix of the mitochondria. .The substrates are coenzymes either NADH or FADH2. .So far, only discussed metabolism of glucose - Know that there are other CHO, And of course fats (lipids)....(Professor changed slides) Other fuel sources: Glucose Glucose - only one of many Other CHO (carbohydrates) Triglycerides: glycerol and fatty acids Lipids (Fatty acids) Proteins (Amino acids) Acetyl CoA is the key: All the "potential energy in these molecules can be.... (Professor changed slides) What happens to the steak or cereal you ate for breakfast? Saliva - mostly amylases (CHOs) some lipases Stomach-acids mainly (thick mucus wall - fuzzy coat) Digestive Enzymes - proteases - in small intestine mostly (pancreas makes most of enzymes, sm intestine some, also liver (makes bile to digest/emulsify the fats) Through (absorbed in) the small intestine, Pass to capillaries Travel to where they will be used. .It is your pancreas that makes most of your digestive enzymes. .Insulin is made by the beta islet cells of the pancreas, and the other enzymes are made by the other part of the pancreas. .When they are broken down that is when you bring in the 3 systems - Glycolysis, Krebs cycle & Oxidative phosphorylation. Figure 3-53 (See diagram) Inter-conversions of the molecules that serve as building blocks and as fuels. **(This diagram is something that you could be tested on)*** .Protein, Glycogen and Fat are the three building blocks. .Not all amino acids can be directly converted to pyruvate they have to be modified. .All proteins have an NH3 and some have NH2's we secrete it as urea in urine. .Glycogen is a storage (only small amount stored as glucose) polymer of glucose. When fed, "glycogenesis" occurs (up arrows). When fasted, "glycogenolysis" occurs (down arrows). .The liver and the kidneys can take one of the products and convert it back to glucose. What controls whether in a given cell, you break down glycogen/glucose to pyruvate OR whether pyruvate is converted to glucose? Concentration of reactants (g or p) Enzymes - control by hormones, concentration. Other fuel sources: .Triglycerides *80% of total body energy content - stored mostly in adipocytes) -Glycerol>glycolysis Glycerol>glycerol-3-phosphate >dihydroxyacetone phosphate -Fatty Acids>Krebs cycle .B-oxidation converts them to Acetyl CoA) (beta oxidation) What is the function of Adipose tissue? .Synthesize and store triglycerides. .Release FA and Glycerol into blood for uptake and use where needed for ATP synthesis. Beta oxidation: the process by which fatty acids, molecules, are broken down in mitochondrion's matrix and/or in peroxisomes to generate Acetyl-CoA, -entry molecule for the Krebs cycle. How are fatty acids modified? Beta Oxidation -Activated Stearic Acid (molecule shown on screen) -Professor is counting the bonds of hydrogen. Two carbon link clipped by enzymes. (molecule shown on screen) Beta-oxidation converts fatty acids into several molecules of acetyl CoA. Figure 3-49, pp88 (See diagram) Lipolysis/Fatty acid catabolism .Lipids/triglycerides: Primary fuel storage molecules .Lipids breakdown>glycerol + FAs (occurs in cytosol) .Glycerol feeds into glycolysis .The long carbon (C) chains of FAs are broken down one at a time into 2-C units by B-oxidation. .Occurs in Matrix of mitochondria .They are then converted to acetyl Co-A .The equivalent of 2 ATP are..... (Professor changed slides) Table 3-10 Characteristics of Oxidative Phosphorylation Entering substrates - Hydrogen atoms obtained from NADH + H and FADH2 formed (1) during glycolysis 2) by the Krebs cycle during the breakdown of pyruvate and amino acids, and 3) during the breakdown of fatty acids Molecular oxygen Enzyme location - Inner mitochondrial membrane ATP production - 3 ATP formed from each NADH + H+ 2 ATP formed from each FADH2 Final products - H2O-one molecule for each pair of hydrogens entering pathway Net reaction - 1/2 O2 + .....(Professor changed slides) How do we get that many ATP? .18 Carbon fatty acid means 9 Acetyl CoA molecules formed. .Will require 8 rounds of B-oxidation. .1 Acetyl CoA=3 NADH+H+, 1 FADH2, 1 ATP >x 9 cycles of Kreb's= 108 ATP .1 turn of B-oxidation= 1 NADH +H+, 1 FADH2 >x 8 cycles of B-oxidation = 40 ATP >=148 ATP (minus 2 ATP to begin B-oxidation) Total = 146 ATP 1 Acetyl CoA -- 3 NADH H -----9 ATP 1 FADH2 ----------------------2 1 ATP ----------------------1 Total 12 x 9 = 108 Energy (ATP) from Fatty Acids relate to Glucose? >36 ATP from 1 glucose >146 ATP from 1 Fatty Acid (18 carbon) >~4 times more energy .When we take molecular weight into account, 1 gram of fatty acids generate ~2.5 times more ATP than 1 gram of glucose. Proteins - Amino Acids -Oxidative deamination: (use AA for fuel) Amino Acid>Keto Acid + co-Enzyme-2H + NH3 ...(Professor changed slides) Snake Venom: Proteins: toxins and enzymes Phosphodiesterases - cardiac system - mainly to lower the blood pressure. Inhibits cholinesterase - loss of muscle control. .... (Professor changed slides) Figure 3-50 Oxidative deamination Amino acids are used as fuels after removal of the amino group. Transamination .One amino acid can be converted to another amino acid by altering the position of some.... (Professor changed slides) Table 3-11 (See slide) Page PAGE 5 of NUMPAGES 5 October 26, 2009 KINE 2011 The Immune System (October 26, 28, 2009) Chapter 18 - but most not covered in two lectures --- use these notes, augmented by the text. .Immunology: the study of the physiological defenses by which our body recognizes itself from non-self. In the process the immune system destroys/renders harmless foreign matter, living and non living. .A collection of mechanisms that protects against disease by identifying and killing pathogens and tumor cells. .Central tenet is concept of self/non-self recognition and distinguishing between them. .Every living organism has some kind of immune system they have some way to protect themselves. .It is a series of mechanisms to protect you from microorganisms that invade your body. .It takes a child about a year to develop its own immune system. .The first year of life of a baby is the most treacherous. .Lupus is a disease where the body attacks itself. Some Functions of the Immune System .Guardian and Protector of the body .Protects against invasion of foreign "agents". .Defends the body against infection. .Responds to infection and destroys the infectious agents. .Removes "unhealthy" cells. .Surveys the body searching out "non-self" (including transformed cells-immune surveillance) Protect Defend Destroy Surveil What does the Immune System protect against? Microbes: bacteria, fungi, parasites, viruses (Viruses (cold, flu) "foreign bodies" (dirt) Allergens: some jewellery, soap powders, pollen Cancer cells (usually) (non self molecules - antigens) Some of the pathologies associated with the immune system -allergy, HIV/AIDS, transplantation) .A virus cannot replicate outside a cell. .It replicates inside the cell. .A bacteria can replicate outside the cells - in the blood stream, in the tissues. .Some bacteria can only replicate inside the cells like Tuberculosis this makes it difficult to irradiate. .Professor talking about transplantations usually it is easier for babies because their immune systems have not developed yet. .Not all transplants are equally immunogenic. .Kidney transplants are the second most common. .HIV/AIDS virus - are hard to develop vaccines because the viruses mutate quickly. .Once you have the virus there are drugs that allow you to control the virus from replicating. .The flu vaccine is about 75% effective. Components of the Immune System (Tissues (organs), Cells, and Chemical messengers (made by cells) (Text, page 647, cells mediating immune defenses) .Most cells are developed in the bone marrow. .All throughout your life you are generating cells in the immune system. .The thymus generates T-cells. .The blood vessels in your body they carry red blood cells that are carrying oxygen and CO2 to your body. .The white cells are lymph cytes and granocytes. .Lymphatic’s generally go from tissue to the rest of the body. .Lymphatics drain into lymph tissue. .The lymph nodes swell once they have been activated to kill the foreign cells. .When you eat an apple there will be stuff on the outside of the apple and your tonsils protects you. .These are really the organs of the immune systems. .They are like cofactors of the immune system. Table 18-1 Cells Mediating Immune System (See chart) Two Arms of defense: Innate and Adaptive (Text calls it nonspecific and specific) .The Innate system is ready and waiting and will fight anything that comes along it is sitting there in your tissues. .The Adaptive system takes days if you have never seen the virus before. .It is specific for antigens and only one region of it. .If it sees it again it has specific cells ready to fight the infection. .The problem with the H1N1 is that there is no Adaptive System that has seen this before. .When viruses go into a cell the H1N1 go deep into the epithelial cells in your lungs. .Once it gets into your lungs it will replicate. .Once you get immunized the body recognizes the virus before it has a chance to replicate. .It is mainly the Adaptive system that works when you have a virus. Main Cells in the Immune System Innate: Granulocytes - Neutrophils, Eosinophils, Basophils Macrophages (Dendritic Cells) NK cells Adaptive: Macophages Dendritic Cells B Cells (activated to become plasma cells) T Cells (cytotoxic-CD8+);helper-CD4+) (NKT Cells) .Children that don't have B + T cells have to live away from others usually in a bubble. .The macrophages and dendritic cells eat virus cells. .Neutrophils are the most common. .Macrophages are called monocytes. .When you cut your finger it swells up this is your innate system. .If you get red lines on the inside of your arms that is an Adaptive response. Why don't antibiotics work on viruses? .Viruses are hidden in cells. .Antibodies work in replication and somehow they stop working. .Antibodies don't work on viruses. Types of white blood cells (how they appear in stained blood smears) (Pictures of slides shown) Innate and Adaptive Masophils & Mast Cells are Rare. .Neutrophils 50-70% Eosinophils 1-3% Monocytes and Macrophages 1-6% T and B Lymphocytes 20-35% Granulocytes (% in a blood smear) Natural Killer (NK) cells (Innate) -contain granules with "killing" functions (like cytotoxic T cells/CD8+ T cells) -can target tumor cells and a wide variety of infectious microbes. (unlike cytotoxic T cells/CD8+ T cells, NK do not need to recognize a specific antigen) -secrete cytokines - e.g. IFN-y (anti-viral cytokine) and TNF - a (Inflammatory cytokine) Macrophages: Both innate (Secrete, phagocytosis) and adaptive (Secrete, phagocytosis, antigen presentation) -secrete and respond to a wide range of inflammatory mediators (cytokines and chemokines-over 10 different molecules! e.g. IL-1 1L-12 IL-6 and TNF - a (Activated macrophages play a key role in host defense against intracellular parasitic bacteria, pathogenic protozoa, fungi and helminths as well as against tumors, especially metastasing tumors). Over 100 known "cytokines" Table 18-2 Features of Selected Cytokines (See chart) .When the flu virus hits you, your body makes Interferon (a cytokine) it is our natural way of fighting it. .Chemokines pull in immune cells to the site and you fight the infection and get better. Some Terminology Antigen: a foreign molecule usually a protein it triggers the specific immune response. Antibodies (these are also termed immunoglobulins, IG) :....( Professor changed slides) APC = antigen presenting cells Dendritic Cells - specialized cells that present antigen MHC = major...... (Professor changed slides) CD4 + T cell = the type of T cell that recognizes antigen in the context of Class II MHC. (also the major cell type HIV infects) CD8+ T cell = the type of T cell that recognizes antigen in the context of Class I MHC. Two Arms of defense: Innate and Adaptive (they call it nonspecific and specific) Innate -Immediate (minutes
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