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Biology 20 Biochemistry Explain how the human digestive and respiratory system exchange energy and matter with the environment • Describe the chemical nature of carbohydrates, lipids, and proteins and their enzymes. Biochemistry Element - A substance consisting entirely of one type of atom, for instance, carbon, hydrogen or oxygen. Elements can combine into compounds to form other substances. Ion – an atom or group of atoms that have a charge Compound - A substance consisting of more than one atom or one type of element, e.g. carbon dioxide is a compound. Biochemistry pH scale - scale is commonly used over a range 0 (acidic) to 14 (basic). • Acid - Substances that have a pH of lower than 7 (neutral) that can dissolve in water. Base - Substances that have a pH of higher than 7 (neutral) that can dissolve in water. Metabolism • Metabolism: All the chemical reactions that occur within the cells. • Monomer: Basic subunit used to build larger molecules. Eg. Amino acids • Polymer: Molecules composed of many basic subunits bonded together – Eg. Many amino acids bond together to form on protein. Polymer: Protein Monomer: Amino acid Chemistry Review • Isomer - A chemical with the same number and types of atoms as another chemical, but possessing different properties. Catabolic Reactants • Complex chemicals broken down into smaller units • Eg. Breaking down food Anabolic Reactions • Small units combine to make larger molecules • Eg. Plants and photosynthesis Dehydration Synthesis • The process by which larger molecules are formed by the removal of water from two smaller molecules. + H20 Hydrolysis • The process by which a larger molecule is broken down into two smaller molecules. Water is taken up at the broken bond site. + H2 0 Chemistry Review • Organic Compounds – contain carbon atoms that are linked together • Inorganic Compounds – do not contain linked carbon atoms. 4 Types • There are 4 major types of organic molecules important in biology. – Carbohydrates • monosaccharides, disaccharides, polysaccharides – Lipids • Triglycerides, Phospholipids, Waxes, Steroids – Proteins • Primary, Secondary, Tertiary, Quaternary – Nucleic Acids (Study these in Bio 30) • DNA, RNA What I need to know about Biochem • Metabolic reactions – Catabolic • Hydrolysis – Anabolic • Dehydration synthesis • Monomers make up Polymers • Isomers have the same formula but a different shape Biochemistry Carbohydrates Types of Carbohydrates Monosaccharides Disaccharides Polysaccharides Carbohydrates • Characteristics – A Carbohydrate can be a single sugar or a polymer of many sugars. – Carbohydrates contain CHO • Carbon, Hydrogen, Oxygen – Ratio of carbon, hydrogen, oxygen = 1:2:1 • Purpose – Source of energy for cellular respiration – Structural material Purposes of Carbohydrates Structural Energy Major structural component of cell organelles, membranes and cytoplasm Produced by photosynthesis, carbohydrates are the major energy source for cells. Energy is released through cell respiration Monosaccharides Types of Monosaccharides • Monosaccharides – Single sugar = C6H12O6 – Three common isomers • (**You don’t have to know the differences in their bonding sites, just that they are the same chemical formula**) • Glucose – blood sugar • Fructose – fruit, honey, twice as sweet as glucose • Galactose – milk sugar, rarely found alone. Types of Monosaccharides Three Monosaccharides Glucose Fructose Galactose Three Monosaccharides Disaccharides Disaccharides • Formed by the joining of 2 monosaccharides – Process called DEHYDRATION SYNTHESIS Disaccharides Dehydration Synthesis Dehydration Synthesis Disaccharides • Formed by the joining of 2 monosaccharides – Process called DEHYDRATION SYNTHESIS – The reverse process is called HYDROLYSIS Disaccharides • Three Common Isomers – Sucrose • Glucose + Fructose • sugar cane, table sugar – Maltose • Glucose + Glucose • found in seeds of germinating plants – Lactose • Glucose + Galactose • Found in milk • Lactose Intolerance is common Polysaccharides Complex Carbohydrates Important Polysaccharides Pronounced kite-in Polysaccharides • Formed by the union of may monosaccharides by dehydration synthesis • Types: – Starch • Multiple sub-units of glucose • Storage form of energy in plants – Glycogen • Branched chains of glucose • Storage of of glucose in animals – liver and muscle cells • High Blood Glucose -- Glycogen formed in the liver • Low Blood Glucose -- Glycogen converted to glucose Cellulose • Structural material found in plant cell walls • glucose is linked together differently compared to starch and therefore only organisms with cellulase can digest it. – Microbes in cow’s first stomach cleave the bonds with cellulase – The cow regurgitates (vomits into his own mouth) – chews again (gross!) – swallows into second stomach (yummy) • What is it good for?? – Roughage -- retains water in feces = soft poo What I need to know about Carbs • Function – Energy storage (Glycogen/Starch) or structure (Chitin/Cellulose) • Types – Monosaccharides: Glucose, Galactose, Fructose (C6H12O6) – Disaccharides: Lactose, Sucrose, Maltose (and which monosaccharides they’re each made of) (C12H22O11) – Polysaccharides: Mostly Starch will be discussed in Digestion Biochemistry Lipids Lipids • Structure – Contains CHO – Ratio of H to O is greater than 2 to 1 • Purpose – Long Term Energy Storage • 1 gram of lipids contains > twice the calories compared to carbohydrates or proteins – Structural Material • cell membranes • cushion for organs • carriers for vitamins • raw material for synthesis of some hormones • insulator Classification of Lipids Types of Lipids • Triglycerides – Formed from 1 glycerol and 3 fatty acids – formed by dehydration synthesis Classification of Lipids Triglyceride Formation Triglyceride Formation Types of Lipids • Triglycerides – Formed from 1 glycerol and 3 fatty acids – formed by dehydration synthesis 1) FAT • • • • • usually from animals saturated fatty acids only contain single bonds Very Stable -- hard to break down solid or semi-solid at room temperature Example: Butter Types of Lipids 2) Oil • usually from plants • polyunsaturated fatty acids have some double bonds between carbon atoms • more reactive than fats therefore more easily broken down • liquid at room temperature • Example: Canola oil Types of Lipids • Phospholipids – Have a phosphate molecule attached to a glycerol backbone Classification of Lipids Types of Lipids • Phospholipids – Have a phosphate molecule attached to a glycerol backbone – Polarized molecule • one side is relatively hydrophilic, other side hydrophobic – Major component of membranes • Waxes – Very stable – Insoluble in water – valuable waterproof coatings for plant leaves, animal feathers and fur Types of Lipids • Steroids – structure = four fused carbon rings Classification of Lipids Types of Lipids • Steroids – structure = four fused carbon rings – Made from cholesterol What I need to know about Lipids • Function – Energy storage (Triglycerides) or structure (Phospholipids – Cell membranes) • Types – Triglycerides (made of 1 glycerol and 3 fatty acid chains) • Saturated – Only single bonds, as many H as possible • Unsaturated – Some double bonds, possible spots to add H – Steroids – Waxes – Phospholipids • Made of C, H, O in varying ratios Biochemistry Proteins Proteins • After water, protein is the most abundant molecule in body – 17% of body weight • 1000’s of types: species specific and individual specific Proteins • Purpose 1) Cell Structure • Major part of muscle, skin, nerves … • Required for the building, repair and maintenance of cell structure. 2) Cell Function • • • • • Chemical messenger -- hormones Transport -- hemoglobin Movement -- contractile proteins Catalysis of cell reactions -- enzymes Defence against foreign substances -- antibodies Proteins • Structure – Contains CHON – Carbon, Hydrogen, Oxygen, NITROGEN • Terms – Protein • A large molecule made of one or more polypeptide chains folded and coiled into a specific shape. – Polypeptide Chains • polymers of amino acids arranged in a specific order and linked by peptide bonds Proteins – Peptide Bond • Covalent bond between adjacent amino acids – Amino Acids • The structural subunit of proteins • 20 Different types • 8 are “essential” – Cannot be manufactured by the body – Must be obtained from food • Structure... Levels of Protein Structure • Primary protein structure – linear arrangement of amino acids in the polypeptide (like beads on a string) – exact sequence of amino acids determines overall protein structure (analogy: different arrangements of letters spell out words with different meanings) – all proteins have primary structure Primary Protein Structure Levels of Protein Structure • Secondary Protein Structure – The coiling and folding of amino acid chains (polypeptides) • coils are like springs • folding produces sheet-like structure • this type of structure is held together by hydrogen bonding between amino acids – Some proteins have lots of secondary structure, some have none Secondary Structure Levels of Protein Structure • Tertiary Protein Structure – The coiled and folded polypeptide is further twisted into n overall 3-D shape • Shape held together by hydrogen bonds, covalent bonds, ionic bonds – Refers to the polypeptide as a whole – Polypeptides may have an overall shape (tertiary structure) that is either • Globular (like a big blob), or • Helical (like a long, coiled spring) Tertiary Structure Levels of Protein Structure • Quaternary Protein Structure – arrangements of polypeptide subunits, when a protein is made up of more than one polypeptide – Held together by hydrogen bonds, ionic bonds, covalent bonds • Example: hemoglobin, many enzymes Quaternary Structure • (a) The primary structure of a protein is the sequence of amino acids in the polypeptide strand. • (b) Hydrogen bonds that form with nearby amino acids coil and fold the polypeptide into α-helices and β-pleated sheets; these constitute the polypeptide’s secondary structure. • (c) The polypeptide folds further to form its tertiary structure. These folds are stabilized by R-group interactions. • (d) The clustering of two or more polypeptides in a tertiary structure generates the quaternary structure of a protein. Protein Changes • Denaturation – Changes in the shape of the protein by physical or chemical factors such as heat, radiation or pH changes. – Protein may uncoil or assume a new shape. – Protein’s physical properties and biological properties are changed. • Coagulation – Permanent change in the shape of the protein • e.g. boiling and cooling egg white What I need to know about Proteins • Function – – – – – – • • • • Structure -- muscles Chemical messenger -- hormones Transport -- hemoglobin Movement -- contractile proteins Catalysis of cell reactions -- enzymes Defence against foreign substances – antibodies Made of CHON (only one with nitrogen) Monomer: Amino Acids Polymer: Polypeptide Chain/Protein Too many kinds to name! Biochemistry Vitamins and Minerals Vitamins • Characteristics: – Organic molecules – Cannot be synthesized from food – Needed in small amounts for bodily functions Inorganic Molecules • Minerals – building materials for cell structures and hormones -- calcium, iron, iodine – coenzymes -- magnesium activates enzymes in protein synthesis – regulating body’s acid-base balance -potassium – regulates the body’s water balance -- sodium Inorganic Molecules • Water – Most abundant molecule in the body – 60% of adult weight – Functions: • excellent solvent • involved in chemical reactions – hydrolysis • maintains constant body temperature Biochemistry Chemical Tests Chemical Test • Chemical tests are used to determine the presence of different types of organic molecules. • Some important tests include: Benedicts Reagent Iodine Test Biuret Sudan IV Dye Benedicts Reagent • Tests for the presence of simple sugars • Negative test: After heating the benedict solution remains blue • Positive test: After heating the blue benedict solution turns yellow to orange. Benedicts Test Negative Test: Blue Positive Test: Orange No simple sugar is present Simple sugar is present Iodine Test • Test for Starch • Negative Test: The iodine solution remains amber when no starch is present • Positive Test: The iodine solution turns blue black when starch is present Iodine Test for Starch Negative Test: Solution remains amber Positive Test: Solution turns blue black No starch in present Starch is present Biuret Test for Protein • Biuret solution is blue • Negative Test: When added to a substance not containing protein, the solution remains blue • Positive Test: When added to a substance containing protein, the substance turns purple Biuret Test for Protein Negative Test: Solution remains blue Positve Test: Solution turns violet Sudan IV & translucence test • Test for fats • If fat is present in the sample tested, a red or pink colour will result Translucence test • The presence of fats can be detected by rubbing samples on a piece of unglazed paper What I need to know about Chemical Tests • We will use these results to complete a lab report later in the unit • You don’t have to memorize the indicators Video Review • Crash Course • Good Cartoon Enzymes What is it?? • Enzymes are PROTEIN molecules. • Protein molecules are composed of one or more amino acid chains, folded into uniquely shaped globs. Enzymes act as CATALYSTS! Catalysts are chemicals that regulate the rate of chemical reactions. Are not consumed or altered during the reaction Activation Energy Activation Energy is the energy input required to initiate any reaction. Activation Energy Activation Energy is the energy input required to initiate any reaction. Enzymes regulate cell activities (metabolism) by lowering the activation energy reactions, therefore, occur more rapidly and at lower temperatures. Activation Energy Activation Energy Activation Energy FUNCTION vs. SHAPE TWO THEORIES 1) LOCK & KEY THEORY • Each chemical reaction requires its own enzyme therefore “one reaction = one enzyme” concept • The enzyme forms a temporary bond with a special molecule called a SUBSTRATE • substrate a molecule on which an enzyme works – A substrate is always… » the substance acted upon » the substance which is changing • Active Site the area of an enzyme that combines with the substrate Get’in Together • When the substrate and the enzyme combine or “join” at the active site, the tandem is called an Enzyme-Substrate Complex. Lock & Key (Con’t) – The ENZYME-SUBSTRATE COMPLEX then separate into product(s) and enzyme Important • Note that: – The enzyme remains unchanged and ready to react again with a new substrate. Important • The substrate has been turned into products. INDUCED FIT MODEL • Improved Theory – 1973 – suggests that the shape of the active site does NOT exactly fit the shape of the substrate – The substrate forces its way into the enzyme – This makes for a tighter fit – The orientation of the substrate molecules in the ENZYME-SUBSTRATE COMPLEX helps speed up the chemical reaction by adding stress to bonds more easily bringing reactive sites physically closer together Induced Fit (Cont’d) Once a bond is formed (or broken) in substrate(s) then products are released and the ENZYME REMAINS UNCHANGED and may be REUSED! A single enzyme can catalyze several million reactions in one minute The same enzyme may also catalyze the reverse reaction The net result is that a one step reaction is converted into a multi-step reaction, therefore, lowering the activation energy – the minimum amount of energy required to initiate a chemical reaction. Naming Enzymes Enzymes are named after the substrate which it acts upon To name an enzyme, usually, the suffix “ase” is added to the end of the substrate name. For example: Substrate Sucrose Lactose Peptide Bonds -Ketoglutarate ... Enzyme Sucrase Lactase Peptidase ????? -Ketoglutarase Regulation of Enzyme Activity METABOLIC PATHWAYS cellular processes that involve many steps are controlled by enzymes one enzyme for each step. Allosteric Activity a change in an enzyme caused by the binding of a molecule Some enzyme’s shape may be altered by a “moderator molecule”. can be a cofactor (mineral) Coenzymes (organic molecules) sometimes even the product molecule. A Moderator Molecule Cofactors Regulation of Enzyme Activity FEEDBACK INHIBITION ***Super Important concept in Biology – also called Negative Feedback** Stops a metabolic pathway the product of an metabolic pathway acts as a moderator on an enzyme in the series, thereby altering its shape (active site) the enzyme cannot combine with the substrate Once the moderator molecule is removed from the moderator site, the active site snaps back to its original shape. Feedback Inhibition Glucose Glucose Glucose Glucose Glucose Glucose Glucose Glucose feedback inhibition • feedback inhibition the inhibition of an enzyme in a metabolic pathway by the final product of that pathway feedback inhibition Factors Affecting Enzyme Reactions • There are four factors that affect the rate at which an enzyme can work. 1) Temperature 2) pH 3) Substrate Concentration 4) Competitive Inhibitor Molecules TEMPERATURE in order for a reaction to occur molecules must collide as temperature increases, collisions increase DOES RATE OF REACTION INCREASE WITH TEMPERATURE??? • NOT NECESSARILY!! Enzymes have an optimal temperature at which the reaction is fastest. Beyond this temperature, the rate of reaction decreases This is because at high temperatures, the unique shape begins to change – denaturation. This results in a loss of the active site Each enzyme has its own optimal temperature Human body approx. = 370C Sperm producing enzymes = 340C This explains why fevers and colds are dangerous pH acidity or alkalinity the lower the number the more acidic the higher the number the more alkaline Enzymes have an optimal pH at which the reaction is fastest Just like with temperature, pH’s out of the optimal range will cause a decrease in rate of reaction shape changes = enzyme denatures. CONCENTRATION Since molecules must collide for a reaction to occur, it is only logical that the more substrates you have, the greater the chance the enzyme will have of combining and reacting with it. The rate does not continue to rise as you add more and more substrate. There is a limit to the amount of enzyme available A substrate cannot join with the active site of an enzyme until it is free. Therefore, once the number of substrate molecules exceeds the number of enzyme reaction sites, the reaction rate levels off. Competitive Inhibitor Molecules Competitive Inhibitor molecules interfere with the enzyme combining with its substrate. – Competitive Inhibitor shaped like substrate COMPETES for active site fits into active site = physically blocks substrate from entering active site enzyme becomes useless Competitive Inhibition Competitive Inhibitor Molecules Examples: Cyanide – binds to enzyme in the Electron Transport Chain preventing formation of ATP. Carbon Monoxide – binds to hemoglobin irreversibly, therefore, no oxygen can be carried Penicillin – binds to enzyme that allows bacteria to make its protective covering, therefore, bacteria becomes susceptible to the immune system and other drugs Video Review • In Depth Review • Cute Cartoon