IB Chemistry 3 Robinson High School Andrea Carver Biochemistry is… The study of the chemical processes occurring in living organisms. Includes processes involving the flow of both energy and information. Deals with biomolecules such as proteins, carbohydrates, lipids, and nucleic acids. Energy: IB Objectives B.1.1 Calculate the energy value of a food from enthalpy of combustion data. Energy Every living cell contains thousands of biological molecules each of which is involved in the interlinked processes of metabolism. Cellular respiration is the oxidative process by which energy stored in food is made available for use by the cell. O2 Starch Protein Rxns of Respiration Glucose Glycogen Fats Energy CO2 + H2O Measuring Energy Production Combustion analysis is used to determine the amount of energy produced from a unit of a particular food. A bomb calorimeter measures the heat of combustion of a reaction. Food is burned within the calorimeter, and heat released raises the temperature of a known quantity of water. Calculation of Energy Release Formula: q=mc∆T q= the energy evolved (J) m= the mass of water (g) c= the specific heat of water (4.18 J/g•K) ∆T= the temperature change of water (K) Example: A 0.78 food sample combusts raising the temperature of 105.10 g water from 15.4°C to 30.6°C. Calculate the energy value of food in kJ/g. Proteins: IB Objectives B.2.1 Draw the general formula of 2-amino acids. B.2.2 Describe the characteristic properties of 2-amino acids. B.2.3 Describe the condensation reaction of 2-amino acids to form polypeptides. B.2.4 Describe and explain the primary, secondary (alpha helix and beta pleated sheets), tertiary , and quaternary structure of proteins. B.2.5 Explain how proteins can be analyzed by chromatography and electrophoresis. B.2.6 List the major functions of proteins in the body. Proteins: Function Structure- Proteins make up many diverse protective, contractile, and supporting structures in the body. Examples: keratin, collagen, myosin, immunoproteins, hemoglobin, casein, mucoproteins Tools- Proteins are valuable operators on the molecular level such as enzymes and hormones. Examples: lactase, insulin Proteins: Structure Amino Acids are the building blocks of proteins. Amino Acids 2-amino acids- Numbering begins with carbonyl carbon and R group is bound to carbon 2. Carbon 2 is also bound to H, NH2, and COOH. R group- defines the amino acid. Amino acids can be classified by the chemical nature of this group (nonpolar, polar, basic, acidic). 20 amino acids occur naturally. Characteristics of Amino Acids Crystalline, high melting points, greater solubility in water than in non-polar solvents. Exist as dipolar ions- contain both positive and negative charges- zwitterions. Amphoteric- can react as both an acid and a base. Amino acids can act as buffers. Isoelectric Point This is the pH at which the amino acid is electrically neutral (typically when the amino acid is a zwitterion). Condensation of Amino Acids Amino acids link together through condensation reactions to form proteins. Condensation reaction- H2O is eliminated as a new bond is formed. Forms a peptide bond. Two amino acids combine to form a dipeptide. Three amino acids combine to form a tripeptide. More amino acids combine to form a poly peptide. The sequence of linked amino acids will determine the nature of the polypeptide=> variety of proteins (millions of possibilities). Structure of Proteins Primary Structure-Number and sequence of amino acids in polypeptide chain. Secondary Structure- Folding of polypeptide chain due to hydrogen bonding between peptide groups. Tertiary Structure- Further twisting, folding of the chain due to interactions between R-groups (side chains). Quaternary Structure- Association between more than one polypeptide subunit. Primary Structure Forms covalent backbone of molecule. Held together by peptide bonds. All other levels of structure determined by primary structure. What determines primary structure of a protein? Secondary Structure Two main types: Beta pleated sheets “side by side” polypeptides Pleated sheets cross-linked Inter-chain H-bonds Flexible, but inelastic Alpha helix Regular, coiled Flexible and elastic Intra-chain H-bonds H-bonds four AA’s apart Tertiary Structure Determines protein’s conformation. Important for function of enzymes, hormones, etc. Most stable arrangement accounting for all possible interactions between side chains. Possible Interactions: Hydrophobic Interactions Hydrogen Bonding Ionic Bonding Disulfide Bridges Quaternary Structure The association of more than one chain in proteins. Analysis of Proteins First, amino acid composition can be determined by hydrolyzing the peptide bonds which link together amino acids in the polypeptide chain. Specific linkages can be hydrolyzed using certain enzymes. Then peptides can be separated based on differences in size and charge using the following techniques. Chromatography Electrophoresis Chromatography Amino acids are treated with a locating reagent to colorize them. A small amount of the mixture is placed at the origin. Stationary Phase- does not move (paper) Mobile Phase- travels taking some sample with it (solvent) Movement of peptide fragments determined by size. Rf= distance traveled by amino acid distance traveled by solvent Specific amino acids have characteristic Rf values. Electrophoresis Separates amino acids based on movement of charged particles. A charge gradient is established on a gel. Proteins migrate based upon charge of side chains present. Proteins settle near their isoelectric points. Carbohydrates: IB Objectives B.3.1 Describe the structural features of monosaccharides. B.3.2 Draw the straight chain and ring structural formulas of glucose and fructose. B.3.3 Describe the condensation of monosaccharides to form disaccharides and polysaccharides. B.3.4 List the major functions of carbohydrates in the human body. B.3.5 Compare the structural properties of starch and cellulose, and explain why humans can digest starch but not cellulose. B.3.6 State what is meant by the term dietary fiber. B.3.7 Describe the importance of a diet high in dietary fiber. Carbohydrates Carbohydrates: Functions Carbohydrate Structure Monosaccharides Monosaccharides: Straight-Chain Forms Monosaccharides: Ring Structures Disaccharides Polysaccharides Starch Glycogen Cellulose Digestion of Polysaccharides Dietary Fibre Lipids: IB Objectives B.4.1 Compare the composition of the three types of lipids found in the human body. B.4.2 Outline the difference between HDL and LDL cholesterol and outline its importance. B.4.3 Describe the difference in structure between saturated and unsaturated fatty acids. B.4.4 Compare the structures of the two essential fatty acids, linoleic (omega-6 fatty acid) and linolenic (omega-3 fatty acid) and state their importance. B.4.5 Define the term iodine number and calculate the number of C=C double bonds in an unsaturated fat/oil using addition reactions. B.4.6 Describe the condensation of glycerol and three fatty acid molecules to make a triglyceride. B.4.7 Describe the enzyme catalyzed hydrolysis of triglycerides during digestion. B.4.8 Explain the higher energy value of fats compared to carbohydrates. B.4.9 Describe the important roles of lipids in the body and the negative effects that they can have on health. Lipids Lipids: Characteristics Hydrophobic, insoluble in water Soluble in non-polar solvents Contain Carbon, Hydrogen, and Oxygen Less oxidized than carbohydrates (more H, less O) Include fats, oils, steroids, and phospholipids Functions: Energy Storage Insulation Protection of Organs Absorption of Fat Soluble Vitamins (A,D,E,K) Structural-Membrane Component Myelin Sheaths of Axons Negative Effects of Lipids •Excess lipids are stored in the body as adipose tissue. •Sometimes excess lipids are deposited into the walls of arteriesAtherosclerosis. •Atherosclerosis (aka hardening of the arteries) can lead to hypertension , stroke, and myocardial infarction. •The image shows the aorta of an individual with atherosclerosis. Cholesterol: Good or Bad? Cholesterol is insoluble in blood, so it is transported as lipoproteins: HDL and LDL. LDL- “bad cholesterol” HDL- “good cholesterol” Lipid Structure Three main types: Triglycerides Phospholipids Steroids Triglycerides Fatty Acids: Saturation Saturated fatty acids have no double bonds. Mono-unsaturated fatty acids have one double bond. Polyunsaturated fatty acids have more than one double bond. Essential Fatty Acids Some fatty acids cannot be synthesized by the body and must be obtained from the diet. These are essential fatty acids. Linoleic acid (omega-6) Linolenic acid (omega-3) Iodine Number Determination of the number of double bonds in a fatty acid based upon its reactivity with iodine. Iodine can add to formerly double bonded carbons (addition reaction). The iodine number is the number of grams of iodine which can react with 100 grams of fat. Digestion of Fats Lipases digest fat via hydrolysis reactions. Structure: Steroids Micronutrients & Macronutrients: IB Objectives B.5.1 Outline the difference between micronutrients and macronutrients. B.5.2 Compare the structures of retinol (vitamin A), calciferol (vitamin D), and ascorbic acid (vitamin C). B.5.3 Deduce whether a vitamin is water or fat soluble from its structure. B.5.4 Discuss the causes and effects of nutrient deficiencies in different countries and suggest solutions. Nutrients Nutrients are necessary for the body and must be obtained from the diet. Recommended Daily Intake is the amount of a given nutrient which must be consumed each day. Macronutrients- nutrients required in large amounts Micronutrients- nutrients required in extremely small amounts Vitamins Vitamins are organic compounds required in small amounts by the body. These compounds must be obtained from the diet. Categorized by solubility: Fat Soluble Vitamins A, D, E, & K Non-polar molecules, hydrocarbon chains or rings Slower absorption Excess can be stored in fat which can be pathological Water Soluble Vitamins C Polar bonds, can hydrogen bond Transported directly in blood Excess can be removed by the kidney Vitamins Vitamin A Vitamin D Vitamin C Malnutrition Results from deficiencies or imbalances in the diet. Broad spectrum of conditions which compromise health. Refers to both nutrient-deficiency diseases and diseases associated with consumption of micronutrient poor, energy dense foods (i.e. diabetes, obesity) Micronutrient Deficiencies Iodine Deficiency Necessary for thyroxine synthesis Goitre Mental retardation Vitamin A Deficiency Necessary for healthy skin and vision Yellow and orange fruits and veggies, spinach, egg yolks Xerophthalmia Possible solution: vitamin A fortification of margarine or rice Iron Deficiency Most prevalent micronutrient deficiency in the world Essential component of hemoglobin Anemia Macronutrient Deficiencies Protein Deficiency Marasmus Kwashiorkor Causes of Malnutrition Lack of distribution of global resources. Depletion of nutrients in the soil due to erosion or misuse. Lack of nutrition education. Over-processing of food products. Use of chemical treatments such as herbicides. Possible Solutions Fortification of staple foods with micronutrients. Availability of nutritional supplements. Genetic modification of food to improve nutrient content. Food labels include content information. Education emphasizing importance of balanced diet and personal responsibility in diet choices. Hormones: IB Objectives B.6.1 Outline the production and function of hormones in the body. B.6.2 Compare the structures of cholesterol and the sex hormones. B.6.3 Describe the mode of action of oral contraceptives. B.6.4 Outline the use and abuse of steroids. Hormones Used for communication within the body by the endocrine system. May be proteins, steroids, modified amino acids, or fatty acids. Produced and secreted into the bloodstream by endocrine glands. Bind to receptors on target cells to produce response. Steroid Hormones Oral Contraceptives “The Pill” typically consists of one or both of the sex hormones, estrogen and progesterone. This provides negative feedback to the pituitary to prevent the production of FSH and LH which normally trigger ovulation. No ovulation = no pregnancy. Typically taken daily, but “morning after” versions are available for emergency use. Uses and Abuses of Steroids Uses: Oral Contraceptives Hormone Replacement Therapy (HRT)- Medications prescribed to replace hormones lost during menopause. Anabolic Steroids (Androgens such as Testosterone)Promote muscle tissue growth following debilitating diseases. Can be abused by athletes. Side effects- Changes in secondary sex characteristics, liver toxicity-cancer Enzymes: IB Objectives B.7.1 Describe the characteristics of biological catalysts (enzymes). B.7.2 Compare inorganic catalysts and biological catalysts (enzymes). B.7.3 Describe the relationship between substrate concentration and enzyme activity. B.7.4 Determine Vmax and the value of Michaelis constant (Km) by graphical means and explain its significance. B.7.5 Describe the mechanism of enzyme action, including enzyme substrate complex, active site, and induced fit model. B.7.6 Compare competitive inhibition and non-competitive inhibition. B.7.7 State and explain the effects of heavy-metal ions, temperature changes, and pH changes on enzyme activity. Enzymes Nucleic Acids: IB Objectives B.8.1 Describe the structure of nucleotides and their condensation polymers (nucleic acids or polynucleotides). B.8.2 Distinguish between the structures of DNA and RNA. B.8.3 Explain the double helical structure of DNA. B.8.4 Describe the role of DNA as the repository of genetic information, and explain its role in protein synthesis. B.8.5 Outline the steps involved in DNA profiling and state its use. The Role of Nucleic Acids Includes deoxyribonucleic acid and ribonucleic acid. DNA stores genetic information. stable structure, contains a “code”, able to replicate Double helix structure RNA enables expression of genetic information stored in DNA. Structure of Nucleic Acids DNA and RNA are polymers of nucleotides. Nucleotides Contain: Pentose sugar (C5H10O5) Phosphate group Nitrogenous base RNA: A,G,C,U DNA: A,G,C,T Ribose Forms from condensation reactions between components. Nitrogenous Bases Purines • Larger • Two fused rings Pyrimidines • Smaller • Single ring Polynucleotides Nucleotides link together via condensation reactions. Linkage occurs between 5’ phosphate and C3 of sugar. DNA Double helix of two polynucleotides held together by hydrogen bonds between bases. 10 bp/turn Turn=3.4nm Base pairing: A-T G-C • Stability • “Code” • Replicable Sugar phosphate backbone Semi-conservative replication DNA Replication Occurs during cell division. DNA Profiling Every person has a unique genome. A person can be identified by DNA Profiling. Applications Identify crime victims Identify suspects Confirm biological relationships Determine relationships between populations to study evolution, etc. Procedure: DNA is extracted and cut using restriction enzymes. DNA is amplified using PCR. Fragments are separated and detected using gel electrophoresis. Autoradiogram is produced. RNA Single stranded poly-nucleotide chain. Less stable than DNA Can cross nuclear membrane Types: Messenger RNA Transfer RNA Ribosomal RNA tRNA The Central Dogma Respiration: IB Objectives B.9.1 Compare aerobic and anaerobic respiration of glucose in terms of oxidation/reduction and energy released. B.9.2 Outline the role of copper ions in electron transport and iron ions in oxygen transport. Respiration Cellular Respiration Oxygen Transport Cellular Respiration: Glycolysis Anaerobic Conditions Aerobic Conditions Summary of Cellular Respiration Oxygen Transport Hemoglobin