Unit 1: Metabolic Processes Are You Ready? SBI4U1 DAY 1 1.1 Chemical Fundamentals Scanning electron micrograph Animation http://micro.magnet.fsu.ed u/primer/java/electronmicr oscopy/magnify1/index.ht ml Atoms of the same element with the same number of protons, but a different number of neutrons Uses of Isotopes • Radioisotopes can be used to help understand chemical and biological processes in organisms. • They can also be used in radiometric dating which is useful in determining the age of fossils • They also have numerous medical applications • Example: A solution of phosphate, containing radioactive phosphorus-32, is injected into the root system of a plant. • Since phosphorus-32 behaves identically to that of phosphorus-31, the more common form of the element, it is used by the plant in the same way. • A Geiger counter is used to detect the movement of the radioactive phosphorus-32 throughout the plant. • This information helps scientists understand the detailed mechanism of how plants utilized phosphorus to grow and reproduce. • Brachytherapy is a form of radiation therapy where radioactive isotopes in the form of small pellets (called seeds) are inserted into cancerous tumours to destroy cancer cells while reducing the exposure of healthy tissue to radiation. • It is currently approved for treatment of prostate cancer and cancers of the head and neck. There are also studies underway to see whether it can be used in the treatment of lung cancer. • In radioimmunotherapy, doctors inject antibodies that have isotopes attached. • The antibodies flow through the bloodstream and deliver the radioactivity by seeking out and latching onto proteins on the cancerous cells. • RIT is used the treatment of blood cell cancers, such as leukemia and lymphoma. It is also being looked at for treatment of prostate, colorectal and pancreatic cancers. Valence electrons are those electrons that are available for bonding. The electrons in the outermost s and p orbitals Orbitals: volumes of space around the nucleus where electrons are most likely found Ionic and Molecular Compounds • Formation of sodium chloride: Na+ [ Cl ] Cl Na + • Formation of hydrogen chloride: H Cl Cl H + A metal and a nonmetal transfer electrons to form an ionic compound. Two nonmetals share electrons to form a molecular compound. Ionic Compounds Ionic compounds consist of a lattice of positive and negative ions. NaCl: Covalent Bond How many electrons are involved in each covalent bond? Double and Triple Bonds • Atoms can share four electrons to form a double bond or six electrons to form a triple bond. N2 : N N O =O O 2: • The number of electron pairs is the bond order. Electronegativity is a measure of an atom's ability to attract a shared electron pair when it is participating in a covalent bond with another atom By calculating the net Electronegativity of the atoms, we can determine the distribution of electrons and the nature of the molecule The Pauling scale of electronegativity Electronegativity • nonpolar bond: electrons are shared equally H 2, Cl2: • polar bond: electrons are shared unequally because of the difference in electronegativity. HCl: Electronegativity • Number assigned to each element (En) • Difference in En helps determine the nature of the bond: ionic or covalent • Covalent bonds can be either nonpolar covalent or polar covalent – • This difference has Biological Consequences Bond Polarity A polar bond can be pictured using partial charges: + H Cl 2.1 = 0.9 3.0 Electronegativity Difference Bond Type 0 - 0.5 Nonpolar 0.5 -1.7 Polar 1.7 Ionic MOLECULAR SHAPE • When atoms form a covalent bond, the valence electron pairs arrange themselves to be as far away from each other as possible. • This change to the orientation of the valence electrons is Hybridization. • Symmetry of shape will also determine polarity of molecule or functional group. •Methane: CH4 – tetrahedral shape – equal 109.5 angle between valence electrons; symmetrical; nonpolar Ammonia: NH3 – pyramidal shape – equal 107 angle between valence electrons; asymetrical shape – polar molecule To determine if a molecule is polar or nonpolar, must consider both electronegativity and shape Which of the following is the essential characteristic of a polar molecule? a.Contains double or triple bonds b.is formed at extremely low temperatures c.contains ions as part of the structure d.has an asymmetrical distribution of electrical charge e.contains the element oxygen Van der Waals forces: •intermolecular forces of attraction Examples: London forces, dipole-dipole forces, hydrogen bonds London forces - weak/temporary/ random charges -gases at room temperature - volatile e.g.; octane Dipole-dipole -between polar molecules -stronger - e.g.; HCl • London forces are weak because (1.) partial charges are involved and (2.) because they are temporary. They arise from the random movement of electrons in atoms and molecules. a) small collection of nonpolar molecules b) a nonpolar molecule may temporarily have a slight excess of electrons in one portion of the molecule c) During the brief interval that these temporarily polar molecules exist, they are attracted to each other •Hydrogen bonds: strongest intermolecular bonds Properties of water are due to hydrogen bonds I. They are responsible for the surface tension properties of water. II. They are responsible for the relatively high boiling point of water. III. They are responsible for adhesion- cohesion IV. The make water a good heat sink. V. The maximum density of water occurs at 4°C Solubility • The solubility of many molecules is determined by their electronegativity and molecular structure. • Sugars, such as glucose, have many hydroxyl (OH) groups, which tend to increase the solubility of the molecule. • Molecules that lack polar covalent bonds, such as lipids, clump together in water because they are excluded from interacting with the polar groups. Hydrophobic http://programs.northl andcollege.edu/biolog y/Biology1111/animat ions/hydrogenbonds.h tml …and hydrophilic -“like dissolves like”; --polar nature; excellent solvent -http://programs.northlan dcollege.edu/biology/Biol ogy1111/animations/disso lve.html Functional Groups • Functional groups are clusters of atoms with characteristic structure and functions. • Generally, they are polar covalent groups • They increase the solubility of a substance in water. • The hydroxyl (OH) groups in glucose are what make this sugar soluble Acids and Bases • pH scale is used to measure • Is an inverse logarithmic scale • pH=7 is neutral • pH 7 means high H+ • pH > 7 means high OH- Conjugate Acids and Bases • Weak/reversible • Act to “absorb” protons or release proton to maintain constant pH If an acid has the formula CH3COOH, then the conjugate base would be CH3COO-. Buffers are compounds that tend to neutralize the pH of a solution by combining with either H+ ions or OH- ions to keep the solution neutral. Buffers play a very important role in most organisms, as many organisms cannot live at pHs that are too acidic or too basic. CH3COOH < -------- > CH3COO- + H+ The acetic acid molecule (CH3COOH) acts as a store of base and acid ions. The acetate ion (CH3COO-) acts like a base which accepts H+ and neutralizes them. The hydrogen ion (H+) acts like an acid which accepts OH- and neutralizes them. In living organisms, buffers maintain pH in the cells within a narrow range, allowing enzymes to function Buffer Animation! http://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/buffer 12.swf Review 1.1 ‘Chemical Fundamentals’ Answer p.23 #4,6,7,8,10,12,14,15 • What type of intermolecular forces of attraction must be overcome to melt each of the following solids? A) ice, H2O (s) B) iodine, I2 (s) 4 a) Hydrogen bonds must be broken to melt ice, H2O (s) , into water H2O (l) . b) London forces must be broken to melt I 2 (s) into I 2 (l) . - the only intermolecular forces that hold nonpolar molecules to one another Is carbon tetrachloride, CCl 4 , and ammonia, NH 3 , polar or nonpolar? 6. Based on VSEPR theory and electronegativity values, carbon tetrachloride, CCl 4 , is nonpolar due to the symmetrical arrangement of its polar C – Cl bonds and ammonia, NH 3 , is polar due to the nonsymmetrical arrangement of its polar N-H bonds. Why is table salt, NaCl (s), soluble in ethanol, CH 3 OH (l), but not soluble in gasoline, C 8 H 18 (l) ? 7. Table salt, NaCl (s), is soluble in ethanol, CH 3 OH (l) , because Na + and Cl – ions are attracted to polar ethanol molecules. Na + and Cl – ions are not attracted to nonpolar gasoline molecules (C 8 H 18 (l) ). What is the difference between a weak acid and a dilute solution of a strong acid? • 8. A weak acid only partially dissociates to release H+ ions, while a strong acid completely dissociates. Describe the components of a buffer and the role each plays in helping maintain a constant pH. 10. A buffer is formed from a weak acid and a weak base in approximately equal concentrations. The weak acid will donate a hydrogen ion to a base, neutralizing it, and its conjugate base will accept a hydrogen ion form an acid, neutralizing it. What is the difference between ionic and polar covalent bonds? 12. Ionic bonds are formed because of a complete transfer of electrons from one element to another element. Polar covalent bonds result from the unequal sharing of electrons between two different elements. 1. Hydrophobic: the tendency of nonpolar molecules to exclude water. Hydrophilic: the tendency of polar and ionic substances to dissolve in water. a) C6H 6 (l) is … hydrophobic b) C2H5OH (l) is … hydrophilic. c) CCl 4 (l) is … hydrophobic 15. What property of water accounts for each of the following observations? a) A steel sewing needle floats on water but a large steel nail sinks. A steel sewing needle floats on water because the surface tension of the water holds it there, while a large steel nail sinks because the force of gravity on the nail is greater than the surface tension of the water. b) Dogs pant on a hot summer day. Dogs pant to cool their bodies. The evaporation of water requires heat, due to its high latent heat of evaporation, which it gets from the dog’s tongue. c) Water creeps up the wall in a flooded room. Water creeps up the walls of a flooded room due to the cohesion of water molecules to molecules in the wall because of hydrogen bonding. d) Hands are usually washed in water. Hands are usually washed in water because water is considered the universal solvent and most substances will be dissolved and washed away. DAY 3 - Carbohydrates. Structure/function. Biological importance. Model kits: build glucose, maltose, amylase, glycogen and cellulose. Relate structure to properties to function 1.2 The Chemicals of Life The following structural formula is representative of which functional group? a.sulfhydryl b.carboxyl c.hydroxyl d. amino e.carbonyl carboxyl The following structural formula is representative of which functional group? a.sulfhydryl b.carbonyl d.hydroxyl d.amino e.carboxyl AMINO The following structural formula is representative of which functional group? a.sulfhydryl b.carbonyl c.hydroxyl d.amino e.carboxyl CARBONYL Biological macromolecules 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids Anabolic reactions •Require energy “endothermic reaction” •Produce big molecules •By removing water and forming new covalent bonds (dehydration synthesis) •Require enzymes Catabolic reactions • Produce energy: exothermic • Break big molecules into smaller • Adding water to break covalent bonds (hydrolysis reactions) • Require enzymes CARBOHYDRATES [CH2O ]n • • • • Monosaccharides: 1 Disaccharides: 2 Oligosaccharides: 3 – 10 Polysaccharides: greater than 10 Function 1. Energy ~ glucose 2. Longer term energy needs/storage ~ glycogen (animals) and starch (plants) 3. Structural ~ cell wall of plants (cellulose) 4. Recognition & communication (cell surface markers & identification of self vs non-self~ glycoproteins) carbohydrates… • Classified based on – Size of base carbon chain – Number of sugar units – Location of C=O – stereochemistry Monosaccharides (various isomers – same chemical formula; different chemical and physical properties) Some important monosaccharides • D-glyceraldehyde: simplest sugar • D-glucose: Most important in diet; common names include dextrose, grape sugar, blood sugar • D-fructose: sweetest of all sugars • D-galactose: Part of milk sugar • D-ribose: used in RNA Glycosidic linkages (ether): covalent bonds holding monosaccharides to one another Dehydration synthesis (mostly 1-4 linkage) - starch -glycogen -cellulose Several simple sugars attached to one another In humans the function of glycogen is to keep glucose available. Glucose in Water Animation • http://www.stolaf.edu/people/giannini/flasha nimat/carbohydrates/glucose.swf Based on location of C=O • Aldose – Aldehyde C=O • Ketose – Ketone C=O Steochemistry: study of the spatial arrangement of molecules • Stereoisomers have – The same order and type of bonds – Different spatial arrangements – Different properties – Many biologically important chemicals, like sugars, exist in stereoisomers. Enantiomers molecules that have opposite spatial configuration and are optically active. Day 4: Lipids • Lipids. Structure/model of fatty acid, glycerol, triglyceride. Saturated, unsaturated, cis/trans: properties and function. Steroids, waxes and phospholipids. Homework • Read and summarize proteins for next class. • http://www.tvdsb.on.ca/westmin/science/sbioac/bioc hem/triglyc.htm • Lipids Animations! • http://www2.nl.edu/jste/lipids.htm Lipids: Also called Fats and Oils Lipid Facts • Fat: Solid at room temperature • Oil: Liquid at room temperature • Contribute 30-50% of calories for Americans • Soluble in organic solvents, i.e., not soluble in water (They are all hydrophobic) • Lipids are primarily consumed for energy • Diverse groups: no basic sub-unit Function 1. Energy storage [fats] long-term (2x energy of CHO’s) 2. Cushions/protects organs e.g.; kidney, reproductive organs, etc. 3. Insulation: helps maintain constant internal temperature 4. Structural: cell membrane -phospholipid - cholesterol (fluidity to memb) 5. Vitamins and Hormones (regulation of biological processes) -steroids -testosterone, estrogen, progesterone -vit. D (co-enzyme) 6. Waxes: waterproof/protective coating When a molecule of glycerol reacts with one or more fatty acids an ester linkage results. The formation of this linkage is a result of a reaction between an alcohol and a carboxylic acid Formation of a triglyceride Fatty Acid Nomenclature Based on: • Number of carbons • Number of double bonds Oleic Acid Saturated • No double bonds • Solid at room temperature • Implicated in coronary heart disease (CHD) • Meats, dairy Unsaturated • Has double bonds • Fluid at room temperature • Less stable to off flavor development • Vegetables, legumes, fish LIPIDS Saturated: only single bonds Unsaturated: double bonds between 1 or more carbons • Polyunsaturated: 2-5 double bonds • Highly Unsaturated: >5 double bonds • Omega 3 Fatty Acids – Good for reducing CHD – High in fish Linolenic Acid, an Omega 3 Fatty Acid Micelle - fatty acids are the main component of soaps, where their tails are soluble in oily dirt and their heads are soluble in water to emulsify and wash away the oily dirt (However, when the head end is attached to glycerol to form a fat, that whole molecule is hydrophobic) Phospholipids • Modified fatty acid • Two fatty acids tails and a cholinephosphate head • Tails are hydrophobic • Head is hydrophilic • Cell membrane (4 ring compounds) Cholesterol Why is cholesterol important in the body? • Hormone production • Membranes • Vitamin D • Absorption of fats Foods high in cholesterol • Organ meats • Eggs • Shellfish Waxes • Extremely hydrophobic • Cutin: cuticle of leaf When one fat molecule is broken down to glycerol and fatty acids, the number of hydroxyl ions consumed in order to neutralize the fatty acids would be a.0, b.3, c.1, d.4, e.2 Fat uses in Foods Flavor • Fried Foods • Popcorn Texture • Shortening (Flakiness) • Moistness Stabilizers (emulfsifiers) • Lecithin • Mono and diglycerides Relationship of Fat and Cholesterol on CHD • CHD is No. 1 killer of Americans • Approximately1 million deaths/year General Agreement • Cholesterol and tryglycerides build up in arteries and reduce blood flow to heart. Hypothesis • Reduce cholesterol and fat in diet and reduce CHD Issues w/ Fat and CHD Cholesterol not only Factor in CHD • Heredity • Stress • Smoking Response from Industry Theory: Produce fat-like substance that has reduced metabolism Examples – Olestra - sucrose polymer • Expected for use in all types of foods • Issues: Anal leakage and vitamin loss EXPERTS SAY... • Lower fat intake to 30% of daily calories • Consume “proper amount” of fatty acids in diet • Have approximately 1:1.5:1 ratio of saturated, monounsaturated and polyunsaturated fats • Dietary fiber may be of some benefit • Some suggest increase intake of Omega 3 Fatty Acids – May reduce blood cholesterol Day 5: Proteins • Functions. Amino acid structure and properties of R groups. Primary, secondary, tertiary and quaternary structure and bonds. Homework: • Read and summarize nucleic acids • http://www.tvdsb.on.ca/westmin/science/sbioac/biochem/am ino.htm Proteins Next to water, protein is the major component of living cells! The 20 amino acids – see pg. 42 Polypeptide structure - Animation http://science.nhmccd.edu/biol/dehydrat/dehydrat.html Essential Amino Acids • Humans can not synthesize them; they are dietary requirements (there are 8) Protein structures Animation http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swf Primary Structure "The sequence of amino acids in the polypeptide chain." Secondary structure The Helix nature of wool is what makes it shrink. The pleated sheet structure is often found in many structural proteins, such as "Fibroin", the protein in spider webs. Tertiary structure Globular proteins -spherical in nature -Common globular proteins include egg albumin, hemoglobin, insulin, and many enzymes. Quaternary Structure Proteins when heated can unfold or "Denature". This loss of three dimensional shape will usually be accompanied by a loss of the proteins function. If the denatured protein is allowed to cool it will usually refold back into it’s original conformation. Dipeptide hydrolysis Day 6 Nucleic acids: DNA and RNA: structure and differences. Bonds in DNA. Nucleoside, nucleotide, purine pyrimidine. Other nucleic acids: ATP, NAD, NADP, FAD p.56 #1,3,4,5 ,6,9,10, 11,13,14, 16 ,17,18,19 Base pairing in DNA anitiparallel Nucleotides (Both Sides of Double Helix) Adenosine triphosphate (ATP): major energy carrier Coenzyme A (CoA) Flavin Adenine Dinucleotide (FAD) Nicotinamide Adenine Dinucleotide (NAD+) Nicotinamide Adenine Dinucleotide Phosphate (NADP+) PRACTICE QUESTIONS A) Structurally, a sulfhydryl group is most similar to which of the following? a.carbonyl, b.hydroxyl, c.carboxyl, d.amino, e.acetyl B) A nitrogen atom would be found bonded to a hydrogen atom in which of the following functional groups? a.sulfhydryl, b.carbonyl, c.hydroxyl, d.amino, e.carboxyl C) In terms of maintaining the shape of an enzyme, the strongest bonds involved are a. covalent (disulfide) bonds, c.dipole-dipole interactions, e.ionic interactions b.hydrogen bonds, d.hydrophobic bonds, D) Which of the following functional groups would be found in a monosaccharide? a. carbonyl and hydroxyl, c.glycosidic and hydroxyl, e.carboxyl an amino b.carboxyl and carbonyl, d.hydroxyl and sulfhydryl, E) Of the following, which is not considered to by a polymer? a. cellulose, b.protein, c.RNA, d.fat, e.starch Name Of Reaction Summary Of Changes dehydration synthesis (condensation) two molecules joined; water removed from the point where the molecule join synthesis of macromolecules for storage of energy or information hydrolysis large molecule split into two smaller ones; water added at the point where the molecules split digestion: breakdown to smaller molecules of fewer kinds for active transport redox hydrogen atoms or electrons transferred between reactants energy storage and transfer in cells acid + base – > water and salt stomach acid neutralized by bile and sodium bicarbonate in pancreatic juice in the duodenum neutralization Example TEXT ANSWERS p.56 1. Why are hydrocarbons all nonpolar molecules? Hydrocarbons are all nonpolar molecules because of the symmetrical arrangement of their C-C and CH bonds. 2. List the elements found in all carbohydrates, indicating the atomic ratio in which they are found. carbon, hydrogen, and oxygen in the ratio 1:2:1 3. A) Define functional group. b) What advantage is conferred to biological molecules by having functional groups? A) In organic chemistry, a functional group is a reactive cluster of atoms attached to the carbon backbone of organic molecules. B) Biological molecules with functional groups are more reactive than molecules without functional groups. 4. Why are monosaccharides more soluble in water than are triacylglycerols? Monosaccharides are more soluble in water than triacylglycerols because of the large number of asymmetrical polar bonds. Carbohydrate (or derivative) Main function Glucose Primary source of energy in most living organisms Starch (amylose) Energy storage in plant cells Chitin Structural carbohydrate in insects, crustaceans, and mushrooms Cellulose Plant cell wall component glycogen Energy storage in animal cells 6. Describe the difference between a condensation reaction and a hydrolysis reaction. A condensation (dehydration synthesis) reaction releases a water molecule in an anabolic reaction, while a hydrolysis reaction adds a water molecule across a chemical bond in a catabolic reaction. 9. Why are glucose and galactose monomers? Glucose and galactose are isomers because they have the same chemical formula (C 6 H 12 O 6 ) but different arrangements of atoms. 10. Why do animals use lipids instead of carbohydrates as energy-storing molecules? First, lipids contain more energy per gram than carbohydrates. Secondly, lipids offer greater thermal insulation than carbohydrates and allow animals to survive in frigid environments. 11. A) How many fatty acids are attached to a glycerol molecule in a triacylglycerol? In a phospholipid? b) What two functional groups react when a fatty acied bonds to a glycerol molecule? A) Three fatty acids are attached to a glycerol molecule in a triacylglycerol and two fatty acids are attached to a glycerol in a phospholipid. B) Hydroxyl and carboxyl groups react when a fatty acid molecule bonds to a glycerol molecule. 13. Distinguish between a polypeptide and a protein. A polypeptide refers to a single chain of amino acids with primary, secondary, or tertiary structures, while a protein consists of one or more polypeptide chains twisted and folded together into a specific shape. The amino acid sequence of a polypeptide chain determines the three-dimensional shape of the protein. 14. B) The functional group found on the R-group side chain is a carboxyl group. C) This amino acid is acidic because of its acidic functional group. 16. State two similarities and two differences between an alpha helix and a beta-pleated sheet. Similarities between alpha-helix and beta-pleated - they determine the secondary structure - they occur because of hydrogen bonding Differences - the type of structure formed (spiral helix vs. flat sheets) - alpha helix is formed by hydrogen bonding between successive amino acids along a polypeptide chain, while a beta-pleated sheet is formed from hydrogen bonds between two parallel polypeptide chains. 17. A) List the four types of bonds that stabilize a protein’s tertiary structure. b) Which of these bonds is the strongest? A) The four types of bonds that stabilize tertiary structure are: - hydrogen bonds (a type of van der Waals force), - disulfide bridges (covalent bonds), - ionic bonds, and -hydrophobic interactions ( a type of van der Waals force). B) The strongest of the above are the disulfide bridges because they are the only covalent bond. 18. Describe two differences between RNA and DNA nucleotides. Two differences between RNA and DNA are the sugar found in the nucleotide, RNA has ribose and DNA has deoxyribose, and that RNA is single stranded while DNA is double. Also DNA contains the nitrogenous base thymine, (T) while RNA contains uracil (U) instead. 19. State the rule for base pairing in DNA, indicating the number of hydrogen bonds that forms in each case. The rule for DNA base pairing is adenine with thymine, forming two hydrogen bonds, and cytosine with guanine, forming three hydrogen bonds. DAY 7: SEE HANDOUT 1.3 An Introduction to Metabolism (DAY 8) Read section 1.3 p.58-68 Answer #2,3,6,7,8 Thermodynamics: the science of energy transformations (flow of energy through living and nonliving systems) All living things require ENERGY – which is the capacity for doing work Forms of energy: •thermal •light •chemical •electrical KINETIC ENERGY • Energy of motion: –Falling water –Pistons in a car engine –Skier going down a hill – examples on a molecular scale include the energy of vibrations, random diffusion, and heat. POTENTIAL ENERGY • stored energy • Example: Molecules of glucose have potential energy, stored in bonds FIRST LAW OF THERMODYNAMICS • Energy can neither be created nor destroyed, but can be transformed from one form to another. • E.g.; during photosynthesis, light energy from the Sun is transformed into chemical energy stored in the bonds of glucose • During cellular respiration, the energy in the bonds of glucose is released and is transformed into new molecules, motion, and heat energy. The Second LAW OF THERMODYNAMICS: Every energy transformation increases the entropy of the universe. • There is ALWAYS some loss of useful energy. The second law of thermodynamics In all processes or reactions, some of the energy involved irreversibly loses its ability to do work. or In any reaction the amount of molecular disorder always increases Entropy is a measure of the randomness or disorder in a collection of objects Entropy increases… • when solids become liquids or gases • Complex molecules react to form simpler molecules (catabolic reactions) • During diffusion Living systems seem to break the second Law of Thermodynamics • Anabolic processes in cells build highly ordered structures (e.g.; proteins and DNA) from a random assortment of molecules (amino acids and nucleotides) in the cell fluids. • On a large scale, living organisms build and maintain highly ordered structures such as cells, tissues, organs and systems, as well as nests, webs and homes. • All of these changes cause the universe to become a little more ordered. But these anabolic processes are coupled to catabolic processes • Which release free energy and thermal energy and increase the entropy of the universe. • Living organisms create order in a local part of the universe at the expense of greater a greater amount of disorder in the universe as a whole. Free energy It is clear that we should be concerned only with energy available to do useful work, so-called free energy or Gibbs energy. Josiah Willard Gibbs (1839 - 1903) The relationship between energy change, entropy change, and the temperature of a reaction is best described in terms of free energy A)Exothermic Reactions • Produce energy (exergonic reactions) • Tend to increase entropy (therefore, spontaneous) – - delta G value • E.g.; cellular respiration Exothermic Reaction During this part of the reaction the molecules are said to be in a transition state. Activation Energy :amount of energy needed to strain and break the reactants' bonds in a biochemical reaction B) Endothermic Reactions •Require energy (endergonic reactions) •Tend to decrease entropy (because they create big/organized molecules) •Are not spontaneous –+ delta G values •E.g.; photosynthesis REDOX REACTIONS • Biochemical reactions are essentially energy transfers. • Often they occur together, "linked" in oxidation/reduction reactions. • Reduction is the gain of an electron. Sometimes we also have H ions along for the ride, so reduction also becomes the gain of H. • Oxidation is the loss of an electron (or hydrogen). • In oxidation/reduction reactions, one chemical is oxidized, and its electrons are passed (like a hot potato) to another chemical. • OIL RIG (oxidation is loss, reduction is gain) • Many metabolic processes (glycolysis, Kreb's Cycle, and Electron Transport Phosphorylation) involve the transfer of electrons by redox reactions. a.the synthesis of glucose in a plant All but one of the following are examples of oxidizing reactions. Which one is not an oxidizing reaction? a.the synthesis of glucose in a plant b.a log burning in a fireplace c.the breakdown of glucose in a cell d.a newspaper turning yellow as it ages e.the rusting of a nail In the following chemical reaction, a oxidation/reduction reaction is occurring. C6H12O6 + 6 H2O + 6 O2 12 H2O + 6 CO2 because electrons are transferred from one substance to another Chemical intermediates - Nucleotides Some compounds contain high-energy bonds, e.g. the bond between phosphate groups of tri- and diphosphate nucleotides Physical energy intermediates An equally common way of storing energy is in the form of potential energy, as an electrical gradient (potential), concentration gradient, or pH gradient. Some proteins (e.g. cotransporters) are able to utilize the flow of ions directly to power their endergonic reactions. ANSWERS - p.58-68 1.3 An Introduction to Metabolism 2. Identify each of the following activities as either anabolic or catabolic. A) protein synthesis is anabolic b) Digestion is catabolic c) DNA synthesis is anabolic d) Photosynthesis is anabolic e) Cellular respiration is catabolic. 3. Metabolism represents the sum of all anabolic and catabolic reactions in a cell or organism. 6. A) an arm raised: a decrease in entropy because potential energy is increased. b) Protein is digested into amino acids in the duodenum: an increase in entropy, because a large number of amino acids ae more randomly arranged than in a protein molecules in which the amino acids are attached to one another in a particular sequence. c) Chromosomes move along spindle fibres: the cells free energy is used to move chromosomes into a more ordered arrangement; entropy decreases as organization increases. 6. D) oxygen diffuses into alveoli in the lungs: an increase in entropy as oxygen molecules trapped in alveoli diffuse into capillaries and move randomly through the circulatory system. e) A cell divides: an increase in entropy as the system is becoming more random, and much of the cell’s free energy is used in cell division; two cells represent a more random arrangement of objects than a single cell 7. Gibbs free energy represents energy that can do useful work. 8. A) Heat death of the universe refers to the state where all the particles and energy of the universe will move randomly, unable to do useful work. All energy will still be present, but it will be uniformly distributed and unable to apply a push or pull to anything. b) Heat death of the universe is related to the death of an organism because a dead organism is unable to do work. Energy is still present, but it cannot perform the work that is necessary to keep the organism alive. 1.4 ENZYMES An enzyme is a biological protein-based catalyst Enzyme nomenclature Enzymes are divided into 6 groups based on the chemical reactions they catalyze. 1. 2. 3. 4. 5. 6. Oxidoreductases Transferases Hydrolases Lyases Isomerases Ligases (synthetases) Enzymes online tutorial • Excellent animations: • http://www.lewport.wnyric.org/jwanamaker/animati ons.htm • http://www.northland.cc.mn.us/biology/Biology1111 /animations/enzyme.html • http://highered.mcgrawhill.com/sites/0072437316/student_view0/chapter8/a nimations.html# Substrate: the reactant that an enzyme acts on when it catalyzes a chemical reaction The Induced-fit model of enzyme-substrate interaction describes a protein as a dynamic molecule that changes its shape to better accommodate the substrate Factors Affecting Enzyme Activity 1.Temperature 2. pH 3. Substrate Concentration 37C is the optimum temperature in most living systems (at high/temperatures enzyme function is altered ~denatured enzyme) - most enzymes work best at pH ~7 (narrow range) - however, some such as “pepsin” have a pH of ~3 - changing the pH will alter the enzymes 3D shape pH Substrate Concentration • As concentration increases, the rate of reaction increases • Maximum occurs when all the enzymes are working cofactors •Inorganic atoms (Zn, Ca, Fe,…) which bind temporarily to enzyme coenzyme •Organic molecules •E.g.; vitamins •Necessary to activate enzyme and allow it to bind to substrate •Also can help weaken bonds in substrates Controlling Enzyme Activity • 1. Regulating transcription/translation . – By regulating transcription/translation, production of enzymes can be turned off/on. – Some end products can act as transcription factors and inhibit the transcription/translation of enzymes • 2. Competitive Inhibition : A substrate mimic (molecule that has the same configuration as the substrate) can enter into ACTIVE SITE and block enzyme action. • Some antibiotics are competitive inhibitors – E.g.; HIV (protease inhibitors) – Penecillin (inhibits a bacteria transpepsidase: cell wall is not built properly) • When bind permanently (poisons or toxins) • When bind temporarily (can be “disloged” by increasing concentration of substrate) Inhibitors • 3. Allosteric Inhibition (Feedback inhibition). Allows an enzyme to be temporarily inactivated. • Binding of an allosteric inhibitor changes the shape of the enzyme, inactivating it while the inhibitor is still bound. • This mechanism is commonly employed in feedback inhibition. Often one of the products of a series of reactions act as an allosteric inhibitor and blocks the pathway. • AKA non-competitive inhibition 3. Regulation of Enzyme Action 4. Allosteric Activators • Substances bind to an allosteric site on enzyme and increase efficiency a) Substrate and enzyme b) Competitive Inhibitor c) Non competitive inhibitor Applications of enzymes for commercial or industrial use! a. starch hydrolysis for the food industry b. proteases to coagulate milk for the manufacture of cheese c. removal of lactose from dairy products for lactose intolerant people d. proteases added to detergents to remove proteinbased stains Enzymes are _________________________ catalysts, and as such they _________________________ a chemical reaction without being _________________________ in the process. Enzymes work by reducing the _________________________. The _________________________ is the reactant that an enzyme act on. This reactant binds to a particular spot on the enzyme known as the _________________________. Enzymes are very _________________________ for the reactant to which they bind. The names of enzymes usually end in _________________________. ANS: protein, speed up, consumed, activation energy, substrate, active site, specific, ase Temperature and pH affect enzyme activity. As with all other reactions, enzymecatalyzed reactions _________________________ in speed with an increase in temperature. However, as the temperature increases beyond a critical point, the protein structure begins to get disrupted , resulting in _________________________ and loss of enzyme function. Every enzyme has a(n) _________________________ temperature at which it works best and activity tends to decrease on either side of this temperature. Most human enzymes work best at around _________________________. Some enzymes require nonprotein _________________________, such as zinc and manganese ions. Other enzymes may require organic _________________________ such as NAD+ and NADP+. A variety of substances inhibit enzyme activity. ___________________________________ are so similar to the enzyme's substrate that they are able to enter he enzyme's active site and block the normal substrate from binding. This process is reversible and can be overcome be increasing the concentration of the enzyme's substrate. Another class of inhibitors does not affect an enzyme at its' active site, they are called ___________________________________ and their effect cannot be overcome by adding more substrate. ANS: increase, denaturation, optimal, 37C, cofactors, coenzymes, Competitive inhibitors, noncompetitive inhibitors Practice! 1. Define catalyst • A chemical that speeds up the rate of reaction without being consumed in the reaction. 2. Draw a labeled free-energy diagram to illustrate the effect of an enzyme on the activation energy of a hypothetical reaction. (Assume it is an exergonic reaction.) 3. What is meant by the statement, “an enzyme cannot affect the freeenergy change of a reaction”? • 5. How does an enzyme lower the activation energy of a biochemical reaction? The enzymes do this by bringing the substrates into the correct geometry and by putting stress on the necessary chemical bonds. 6. How do competitive enzyme inhibition and noncompetitive enzyme inhibition differ? A competitive inhibitor binds to the active site of an enzyme, preventing the substrate(s) from binding. In this case, the inhibitor competes with the substrate for the active site. A noncompetitive inhibitor attaches to an enzyme at a binding site other than the active site. This causes a conformational change in the enzyme’s protein structure that causes a loss of affinity of the active site for its substrate. 8. What happens to an enzyme after it has catalyzed a reaction? After an enzyme catalyzes a reaction, it will catalyze the same reaction again. For an exothermic reaction, H is negative. For an endothermic reaction, H is positive.