Biochemistry B.1-Introduction Understandings

- Shapes and structures of biomolecules define their functions. - Metabolic processes take place in aqueous solutions in a narrow range of pH and temperature. - Anabolism is the biosynthesis of complex molecules from simpler units that requires energy. - Catabolism is the biological breakdown of complex molecules that provides energy for living

organisms. - Condensation reactions produce biopolymers that can be hydrolysed into monomers. - Photosynthesis transforms light energy into chemical energy of organic molecules synthesized

from carbon dioxide and water. - Respiration is a set of catabolic processes that produce carbon dioxide and water from organic

molecules. What is biochemistry? Biochemistry: chemical processes in living cells at the molecular level. Metabolism: all the chemical processes that take place within a living organism to maintain life. Anabolism: the biosynthesis of complex molecules from simpler units that usually requires energy. Catabolism: the breakdown of complex molecules in living organisms into simpler units that is usually accompanied by the release of energy. Metabolic pathway: a biochemical transformation of a molecule through a series of intermediates (metabolites) into the final product. What drives metabolism? Anabolic reactions: o Increases the complexity and order of biochemical systems and thus reduce their entropy. o Can not be spontaneous. o They require energy, which can be supplied by processes such as catabolic reactions and photosynthesis like in plants and cellular respiration for humans.

- Life functions of all organisms are dependent on a balance between anabolic and catabolic processes within their cells, intake of nutrients, excretion of waste products, and exchange of energy within the environment.

- The variety of metabolic pathways allows living organisms to adapt to the constantly changing world.

Molecules of Life - The primary chemical element is carbon.

o It's relatively small size, moderate electronegativity, and the electronic configuration of the outer shell

o Carbon can form up to four single or multiple covalent bonds o High energy bonds – helps with its stability and reactivity o Unlimited number of possible combinations of carbon to form inorganic compounds (CO2), biopolymers (proteins) or even nucleic acids Water: Solvent, reactant, and product

o Most common types of biochemical reactions are: condensation, hydrolysis, oxidation and reduction o Water can be both the solvent and the reactant or product o Biopolymers are formed by condensation reactions (water is released as a by-product) o Up to 65% of the human body mass is composed of water o Biochemical reactions occur in highly controlled aqueous environments where most of the reactants,

products and catalysts (enzymes) are water soluble or form soluble complexes with other molecules. The nature of biochemical reactions

o The reactions responsible for the synthesis and hydrolysis of peptides and proteins, fats and phospholipids, nucleotides and nucleic acids, and many other biologically important molecules are very similar.

o Biochemical reactions usually proceed very fast and with near quantitative yields at body temperature. This action is caused by enzymes (highly specific and efficient biological catalysts). Life and Energy Oxidation and reduction o Proceed stepwise and involve a series of metabolites that transfer and store energy in chemical bonds. o Redox can be described in terms of oxidation numbers, transfer of electrons, or combination with certain elements (oxygen and hydrogen) o In aqueous environments, or where water is prevalent, scientists rely on half equations. o Hydrogen atom are usually lost or gained in pairs, and a single oxygen atom is added to or removed from a molecule at each metabolic step Photosynthesis, respiration and the atmosphere Photosynthesis: the biosynthesis of organic molecules from carbon dioxide and water using the energy of light. Respiration: the metabolic processes that release energy from nutrients consumed by living organisms. Aerobic Respiration: the reverse process of photosynthesis, in which carbon dioxide and water are formed from organic molecules and oxygen. Anaerobic Respiration: the catabolism of organic compounds that does not involve molecular oxygen as an electron acceptor.

o Photosynthesis and respiration are responsible for global balance of oxygen and carbon dioxide o Nearly all the earth’s oxygen is a by-product of photosynthesis, the process that started over two billion

years ago in blue-green algae.

o Photosynthesizing bacteria consumed most of the atmospheric CO2 and made earth habitable for higher life forms – plants, humans and animals.

o Over the past half a million years the level of CO2 in the atmosphere has remained almost constant (0.02 – 0.03%)

o Human activities are increasing the CO2 emissions and as a result, in 2013 the CO2 level rose to 0.04% and continues to rise by 2ppm per year, leading to global warming and other climate changes.

o Biochemical studies allow us to predict the future impact of these changes. B.2 – Proteins and Enzymes Understandings

- Proteins are polymers of 2-amino acids, joined by amide links (also known as peptide bonds) - Amino acids are amphoteric and can exist as zwitterions, cations and anions. - Protein structures are diverse and can be described at the primary, secondary and tertiary and

quaternary levels. - Three- dimensional shapes of proteins determine their roles in metabolic processes or as

structural components. - Most enzymes are proteins that act as catalysts by binding specifically to a substrate at the active

site. - As enzyme activity depends on the conformation, it is sensitive to changes in temperature, pH,

and the presence of heavy metal ions. - Chromatography separation is based on different physical and chemical principles.

The central role of proteins in biochemistry

o Proteins are the most diverse and abundant class of biopolymers, responsible for over 50% of the dry mass of cells.

o The role of proteins – transport and sensory functions, structural integrity and virtually all other molecular aspects of life.

o Simple proteins are linear polymers of 2-amino acids. o The –COO- group in the zwitterion is the basic centre that can be protonated in strongly acidic solutions

and produce the cationic form of the amino acid o The exact ratio of the cationic, zwitterionic and anionic forms of an amino acid depend on the pH of the

solution and the nature of the side chain. o At pH = 6, amino ac The structural units of proteins are joined together by amide linkages (peptide

bonds). o Shorter polymers composed of less than 20 residues of 2-amino acids are called peptides. o “polypeptides” refers to longer peptides or small proteins with 20-50 structural units o Some biochemists differentiate polypeptides and proteins by their ability to fold and adopt specific

conformations in aqueous solutions. 2-amino acids and peptides

o From more than 500 naturally occurring amino acids, only 20 are proteinogenic – used by living organisms as building blocks of proteins.

o Structures of amino acids all have: an amino group, and a carboxyl group added to the same carbon o According to IUPAC nomenclature, this carbon is numbered C-2, so all proteinogenic amino acids are

called “2-amino acids” o The substituent R, often refer to a side chain (a hydrocarbon fragment or contain various functional

groups) 2-Amino acids as zwitterions o 2-amino acids are amphoteric species that contain a weakly acidic group (-COOH) and a weakly basic group (-NH2) in the same molecule o In neutral aqueous solutions, both the carboxyl group and the amino group are almost completely ionized. o This ionization can be represented as an intramolecular neutralization reaction or a migration of a proton (H+) from the –COOH to the –NH2 group o The resulting species with two ionized groups has net zero charge and is called a zwitterion (from the German Zwitter, which means “hybrid”) o The –NH3

+ group in the zwitterion is the acidic centre that can lose a proton in strongly alkaline solutions and produce the anionic form of the amino acids with neutral side chains (R=CH3, CH2, OH, etc.) exist almost exclusively with zwitterions, while the concentrations of cationic and anionic forms are negligible. The sum of positive and negative charges of all forms of the amino acid is zero, this pH is called isoelectric point (pI) o Typical range for the pI of an amino acid is: 5.5 to 6.3, however, the presence of an additional carboxyl group in the side chain lowers the pI to 2.8 – 3.2, whereas extra amino acids increase the pI to 7.6-10.8 o pH‹ pI

· the net electric charge of the amino acid becomes positive · the concentration of the cationic form increases · zwitterion concentration decreases

o pH› pI · the amino acid has a negative net electric charge · more anionic and fewer zwitterionic species present in the solution

o zwitterions are abundant in a range of pH values o cationic and ionic forms become dominant only in strongly acidic and strongly alkaline solutions o the ability of amino acids and their derivatives (peptides and proteins) to exist in various forms neutralize

both strong acids and strong bases is important in maintaining the acid-base balance in living organisms. Experimental conditions for paper chromatography

o Standard chromatographic paper consists of the polysaccharide cellulose that readily absorbs polar compounds.

o If a non-polar solvent (eg. A hydrocarbon), highly polar amino acids will remain at the start line (Rf = 0) and no separation will be achieved.

o A highly polar solvent (eg. Water), amino acids will stay in the mobile phase and travel with the solvent front (Rf = 1)

o The most common solvents used for amino acid separation are: polar alcohols, esters or chlorinated hydrocarbons

o If two or more components have similar Rf values, the experiment can be repeated by rotating the paper through 90⁰ and using a different solvent, pH or even separation method, such as gel electrophoresis. Peptide Bonds

o Molecular (non-ionized) forms of 2-amino acids do not exist, they are theoretical abstractions that allow us to simplify reactions schemes and the nomenclature of large organic molecules.

o 2-amino acids may undergo condensation reactions and produce peptides. o When the –COOH group of one amino acid reacts with the –NH2 group of another amino acid, a molecule

of water is released and a peptide linkage (amide linkage/amide bond) is formed. Naming Peptides

o Formed by changing the suffixes of all but the the last amino acid residue from “ine” or “ic” to “yl” (i.e. alanine + serine = alanyl-serine)

o Abbreviated names of amino acids can be joined together by dashes (i.e. Ala + Ser = Ala-Ser) o Order is important in naming, as reversal of order signifies another amino acid o The first amino acid in a peptide has a free –NH2 group, this is the N-terminal o The last amino acid has an unreacted –COOH group, this is the C-terminal o Both N- and C- terminals can further participate in condensation reactions o The synthesis usually begins from the N-terminal

The Hydrolysis of Polypeptides

o In the presence of strong acids, strong bases or enzymes, peptides can be hydrolyzed o The hydrolysis requires one molecule of water o In a peptide with n amino acid residues, the number of peptide linkages will be n - 1 and therefore n –

1water molecules will be needed to balance the equation.

B.3 Lipids ● Fats are more reduced than carbohydrates, therefore they yield more energy when oxidized ● Triglycerides = glycerol + 3 fatty acids with ester links (by condensation) ● Fatty acids can be saturated, monounsaturated, polyunsaturated ● Phospholipids are derived from triglycerides ● Lipids are structural components of cell membranes, energy storage, transport, hormones,

thermal & electrical insulation Lipids in Living Organisms

● Naturally occurring, largely non-polar, insoluble in H2O ● Defined in terms of properties, not structural/chemical behaviour

● Most are relatively small & hydrophobic, tend to form large assemblies with regular structures held together by van der Waal's forces

Fatty Acids & Triglycerides

● Fatty acids (long-chain unbranched carboxylic acids) ● Free fatty acids are not classified as lipids but are components of triglycerides &

phospholipids ● Most contain an even # of C atoms (typically 4-18, even up to 28) ● Saturated F.A.: only single C-C bonds, general formula of Cn H2n+1 COOH ● Unsaturated F.A.: One or more –CH=CH- groups, described as mono/polyunsaturated ● Naturally occurring unsaturated fatty acids = cis-transfigurations ● Unwanted by-products in food processing = trans-configurations

Physical Properties of Fatty Acids

● Molecular mass increases melting points (-8°C- +70°C) ● Saturated F.A. with 10+ C atoms are solid at room temp. b/c of close packing & multiple van

der Waal's forces ● Double C=C bonds distorts the chain & prevents close packing (reduce intermolecular forces

& melting points, therefore all unsaturated F.A. are liquid at room temp. ● Triglycerides with double C=C bonds have similar molecular packing)

Essential Fatty Acids

● Certain polyunsaturated fatty acids can't be synthesized in the body & are found in food ● 2 essential fatty acids, linoleic & linolenic, contain C=C bonds on the 6th (omega six) and 3rd

carbon (when 1st carbon is the farthest from the carboxylic group) ● Source of omega 6 fatty acids: plants, seeds, vegetable oils ● Source of omega 3 fatty acids: fish, shellfish, flaxseed oil ● Essential fatty acid deficiency= dermatitis, heart disease, depression

Triglycerides

● Fatty acids tend to form esters w/ polyfunctional alcohols like triglycerides (most common) ● Physical properties depend on the nature of fatty acid residues on the molecule ● Like free fatty acids, saturated triglycerides= solid at room temp. (fats) & triglycerides w/

unsaturated fatty acids = liquid at room temp. (oils) The Iodine Number

● Naturally occurring fats & oils are mixture of triglycerides w/ residues of various F.A. ● Exact amounts of triglycerides in a mixture is unknown ● Degree of unsaturation of fats & oils = average # of C=C bonds per unit mass of fat/oil,

determined by reaction of triglyceride mix w/ elemental iodine (combines w/ C=C bonds via electrophilic addition)

● Reaction mixture will stay colourless until iodine is consumed by triglyceride, then turns yellow/brown, reaction is then complete & C=C bonds have reacted with I2

● IODINE NUMBER: max mass of I2 in grams that can be consumed by 100g of triglyceride/unsat. Substance

● Animal fats have few double bonds, therefore low iodine number (40-70) Hydrolysis of Triglycerides

● In body, ester bonds in triglycerides are cleared by lipases from pancreas & small intestine ● In the lab, they hydrolyse by hot aqueous solutions of strong acids/bases ● Triglyceride + acid = glycerol + 3 fatty acids, triglyceride + base= salt + 3 fatty acids

Rancidity of Fats

● The chemical/biological decomposition of fats & oils in food is largely responsible for odours in rotting food

● Hydrolic Rancidity: is caused by the hydrolysis of ester bonds in triglycerides when food is exposed to moisture/high water content

● Hydrolysis is accelerated by enzymes, acids (organic), high temps. ● Butyric & other short fatty acid chains are the products of H.R. and increase the rate of

hydrolysis (autocatalytic process) ● H.R. can be prevented by keeping food at low temps. & reducing water content ● Microbial Rancidity: enzyme catalysed by hydrolytic rancidity caused by microorganisms

(prevented by sterilizing food & reducing lipase activity) ● Oxidative Rancidity: C=C bonds are cleared in unsat. Fatty acids and triglycerides by free

radical reactions w/ molecular oxygen (accelerated by sunlight & prevented by light-proof packaging, O2 free environment + antioxidants which are reducing agents, readily by molecular O2 or free radical intermediates, terminates chain reactions and oxidation processes)

● Free-radical oxidation of oils produces aldehydes + keytones w/ odours ● SPONIFICATION: alkaline hydrolysis of fats, fat/oil is treated w/ hot solution of NaOH ● Sponification number: mass of KOH in mg required for hydrolysis of 1g of fat

Lipids & Health

● Fats & oils are important in our diet, yet excessive amounts can cause obesity, heart disease and diabetes (dietary fats & oils must have balanced saturation & level of essential fatty acids)

Calculated Energy Content

● Energy of food can be calculated by % of main ingredients OR a calorimeter ● Bomb Calorimeter: food of known mass + O2 is combusted, released energy is absorbed by

water (calculations involve ΔT, mass of H2O & heat capacity of calorimeter)

Phospholipids

● Structurally similar to triglycerides except one fatty acid is replaced by phosphate group ● Can be hydrolysed into glycerol, phosphoric acid + fatty acids/salt by acids, bases or enzymes ● Polar phosphate group & 2 non-polar hydrocarbon makes phospholipids amphipathic ● Makes bilayers when in aqueous solutions= maximizes van der Waal's interactions between

hydrocarbon tails & allows heads to form H-bonds and dipole-dipole w/ water & each other (allows stability & repairs to be done)

● Hydrophobic nature makes bilayers impermeable for ions & polar molecules, but proteins & steroids in cell membrane control transport

Steroids

● Class of lipids w/ 3 six-membered & 1 five-membered hydrocarbon rings ● Carbon atoms in 4 ring structure (steroidal backbone) ● Almost all steroids have 2 methyl groups attached to the steroidal backbone at 10 & 13,

functional groups at 3 & 17, C=C bonds at 4,5 and 6 ● Ex. Cholesterol: 2 methyl at 10 & 13, hydroxy at 3, C=C bond between 5&6, hydrocarbon

substituent at 17 ● Essential component of cell membrane & main precursor of steroidal hormones (increase in

rigidity & regulate permeability = by hydroxyl group H-bond to phosphate groups of phospholipids, non-polar hydrocarbon backbone & substituent at 5-membered ring= van der Waals' w/ fatty acids=very hydrophobic, transported as lipoproteins=lipid-protein complex)

● Density & solubility of lipoproteins decrease w/ increasing lipid content so HDL (more stable, less deposition in blood) carry less than LDL

Steroid Hormones

● Most steroids are hormones; chemical messengers that regulate metabolism & immune functions (corticosteroids), sexual characteristics & reproductive functions (sex hormones), synthesis of muscle & bone tissue (anabolic steroids=synthetic drugs that mimic testosterone & other hormones that increase protein synthesis & cellular growth, especially in bones & muscles)

B.4 Carbohydrates Intro

● Carbohydrates are a family of O2-rich biomolecules that are involved in metabolic reactions of energy transfer

● General formula: Cn (H2O)m

● Can be mono/di/polysaccharides = because of # of carbon chains ● Monosaccharides w/ 5 or 6 carbon atoms = pentoses/hexoses ● If carbonyl group is connected to terminal carbon= is an aldehyde called aldose, if carbonyl is

attached to 2nd carbon = ketose (ketone sugar) ● # of C atoms & functional group type are sometimes combined ex. Ribose aldose + pentose =

aldopentose

● Carbonyl group + hydroxyl groups make monosaccharides straight, unstable & undergo intramolecular nucleophilic addition reactions which produce 5 or 6 membered cyclic forms of monosaccharides

● Deoxysugars have 1 less O atoms than a normal carbohydrate w/ same carbon chain length ● Each cyclic form of monosaccharide can exist as 2 stereoisomers (alpha/beta forms) ● Haworth projections emphasize nature & position of functional groups

Importance of Glucose

● Most common monosaccharide, main product of photosynthesis, primary source of energy for cellular respiration

● Important intermediate in metabolic processes of mono/di/polysaccharides, amino acids, vitamins)

Reducing Sugars

● Redox properties of monosaccharides depend on position of carbonyl group ● Glucose & aldoses are reducing sugars: terminal carbonyl groups are oxidized under mild

conditions ● Can be detected by Fheling solution= potassium tartrate, Copper (II) sulfate, NaOH= turn

from blue to red in the presence of anabolic OR Benedict's reagent= copper (II) sulfate, sodium citrate & sodium carbonate becomes red from green

Disaccharides

● Condensation reactions of monosaccharides form disaccharides (ex. 2 glucose = maltose + water)

● Oxygen bridge between the two = glycosidic link/bond ● Sucrose= alpha glucose + beta fructose, lactose=galactose + glucose, maltose = glucose +

glucose ● Lactose+maltose produce red when heated w/ Fehling's/Benedict's solutions (therefore

aldehyde groups) ● Even though cyclic form is more stable in solution, equilibrium shifts towards open chain

form b/c it is oxidized by Cu (II) ions & continues to shift until all molecules disaccharide is oxidized

● Sucrose gives negative reaction to Fehling's & Benedict's solution= C-1 atom in f=glucose and C-2 atom in fructose are involved in glycosidic bond

● Formation of disaccharides is reversible by acids/enzymes= hydrolysed Polysaccharides

● Produced by polycondensation of monosaccharides polymers of glucose: amylose (glucoses connected by 1,4-glycosidic links) + amylopectin (glucoses connected by 1,4 and 1,6- glycosidic links)

● Found in all green plants (primary energy storage molecules, and it is the most common carbohydrate in human diet)

● With enzymes= (amylase in salivary glands, pancreas, small intestine) or strong inorganic acids= starch can be hydrolysed into glucose

● Molecular masses of amylose + amylopectin are both large, they are often represented as indefinite chains of glucose, therefore # of H2O molecules needed for hydrolysis are equal to # of monosaccharides amylose + nH2O = nC6H12O6 glucose (equations must always be balanced)

● Oligosaccharides=shorter-chain polysaccharides w/ 10 monosaccharide fragments

The Iodine Solution for Starch ● In aqueous solutions of KI elemental iodine forms orange tri- and polyiodide ions: ● KI(s) = K+(aq) + I- I- (aq)+ I2 (s)= I3

- (aq) Colourless orange

● When orange solution is added to starch, tri- and polyiodide ions react with amylose (becomes blue-black)

Glycogen & Cellulose

● Short term energy store in the form of glycogen in the human body ● Similar to amylopectin but more densely branched & contains up to 1 million of glucose

residues ● Concentrated in liver & muscles where it is hydrolysed into glucose ● Cellulose (polymer of glucose) is the major structural polysaccharide in plants and part of

healthy diet B.5 Vitamins What are vitamins ? -Organic molecules needed for some enzymes to function properly To act as antioxidants, getting rid of free radicals that can cause DNA mutations -Inorganic molecules, by the way, are minerals History -1795, British Navy ships carried a mandatory supply of limes or lime juice to prevent scurvy among the sailors – they were given the name “limeys” -Japanese Navy gave sailors whole grain barley to ward off beriberi -It wasn’t til 1912 that people knew why these “prescriptions” worked to prevent diseases Vital-amine -Casimir Funk named vitamins – vital amines because they were compounds that contained nitrogen (amines contain nitrogen) and were vital for health Along with Frederick Hopkins, they came up with the idea that scurvy and beriberi were diseases that resulted from the deficiency of certain compounds that could be found in foods. Important Vitamins

-There are 18 essential vitamins and minerals for one to maintain a healthy diet (IB only wants these 3) -Vitamin A (retinol) -Vitamin C (Ascorbic Acid ) - Vitamin D (Calciferol) Vitamin Classification - Fat-soluble vs Water soluble Too much of a water soluble vitamin = ok, comes out in urine Too much of a fat soluble vitamin = sickness because it doesn’t dissolve in your urine readily and gets stored in your body. -Fat soluble vitamins: All Dogs Eat Kibbles Vitamin A -Required for the production of rhodopsin (light-sensitive material in the rods of the retina). -Too Little: Nightblindness Xeropthalmia –have difficulty producing tears Effects about 500,000 children in underdeveloped nations Dry mucous membranes - Too Much: Makes you think you have a brain tumor Headache, vomiting, nausea, abnormal vision, loss of hair Some precursors can make you turn orange How do we get Vitamin A ? - 2 Chemicals: Retinoids and carotenoids Retinoids – body can use right away Carotenoids – body can change it into a retinoid Beta-carotene Carotenoids don’t get stored in liver -Foods with 25% of your RDA for Vitamin A Cereal 1oz, oatmeal 2.3 cups Fruit: apricots, canteloupe, mango (1/2 c) Veggies: carrots, kale, peas, sweet peppers (1/2 c cooked) Meat: Liver 3oz Milk: 2 cups Vitamin C -Required for Production of collagen: the protein of connective tissue. Antioxidant

Protects immune system, helps fight off infection, reduces allergic reactions -Too Little: Scurvy (bleeding gums; tooth loss; nosebleeds; bruising; painful or swollen joints; shortness of breath, increased susceptibility to infection, skin rashes; muscle pains, slow wound healing) -Too Much: More than 1000 mcg may cause upset stomach, diarrhea, or constipation How do we get Vitamin C ? -On the label, look for: Sodium ascorbate Isoacrobate Ascorbic acid -Foods with 25% of RDA Cereal: 1 oz Meat: Liver 3oz Fruit: Canteloupe, grapefruit, mango, orange, strawberries, ½ c. Veggies: Asparagus, broccoli, brussel sprouts, kale, kohlrabi, sweet peppers . Vitamin D -Required for the uptake of calcium and phosphorus from food. -Too little: can cause weak bones (Rickets) in children In adults: osteomalacia (soft bones, fracture easily) -Too much: Kidney stones and hard lumps of calcium in muscles and organs Headache, nausea, vomiting, high blood pressure, retarded physical growth and mental retardation in children, fetal abnormalities How do we get Vitamin D? -Required for the uptake of calcium and phosphorus from food. -Too little: can cause weak bones (Rickets) in children In adults: osteomalacia (soft bones, fracture easily) -Too much: Kidney stones and hard lumps of calcium in muscles and organs Headache, nausea, vomiting, high blood pressure, retarded physical growth and mental retardation in children, fetal abnormalities Fortified Foods -Foods are fortified to provide us with the nutrients we need to stay healthy Ex: milk is fortified with vitamin D

-A precursor to vitamin D is extracted from plants, then irradiated to make an active form of Vitamin D, then it is added to food Cooking and vitamin absorption ? -Studies show that cooking foods can cause a decrease in the amount of vitamins in the food Water soluble vitamins dissolve in cooking water Some vitamins are broken down by heating B.6 Biochemistry and the environment Xenobiotics -Xenobiotics are chemical compounds that are found in a living organism, but which are foreign to that organism. Examples Include:Drugs, including antibiotics such as penicillin ,Food additives, Pollutants,PCB’s and dioxins,Insecticides, such as DDT,Heavy Metals, such as mercury and lead ions,Hormones, such as estrogens,Plastics, such as PVC Xenobiotic Pathways -Fat Soluble:

- if the xenobiotic cannot be modified in the organism it may build up in the cells. The increasing concentration of the substance in an organism is known as bioaccumulation. Bioaccumulation vs. Biomagnification -The increasing concentration of the substance in an organism is known as bioaccumulation. -Biomagnification refers to the increase in concentration of a xenobiotic substance in a food web.

Bioaccumulation Examples: Examples: 1)Methyl Mercury Non-polar, cross into the brain leading to mercury poisoning 2) Tetraethyl Lead Non-polar, accumulates in fat tissues 3)PCBs Highly-stable, toxic and carcinogenic, xenoestrogens 4)Pharmaceutically Active Compounds: a)Antibiotics b)Painkillers c)Chemotherapy Drugs d)Hormones (xenoestrogens): PCB and Bisphenol A -For a) through c) - Sewage treatment is not very effective at removing these from wastewater Biomagnification Examples -A well-studied example of this is the insecticide DDT, dichlorodiphenyltrichloroethane. Effective insecticide against mosquitoes used during WWII to prevent the spread of malaria Fat-soluble and does not undergo metabolic breakdown. Banned in the 1970’s because of its effect on bird populations thinning eggshells. -Other examples include dioxins, PCBs and heavy metals such as mercury and uranium. Amelioration: Responses to Xenobiotics -Clearly, the widespread existence of xenobiotics in organisms and in the environment is a major cause of concern for human health and for biodiversity. Amelioration refers to approaches that seek to lessen the problems and improve the outlook.

- Example #1: Host–guest chemistry This involves the synthesis of a host molecule which is able to bind non-covalently to a guest molecule, and form a supermolecule. In essence the host, the larger molecule, is analogous to the enzyme, and the guest to the substrate. The forces within the supermolecule, like those in enzyme–substrate complexes, include ionic bonds, hydrogen bonds, van der Waals’ forces, and hydrophobic interactions. Host–guest chemistry can be applied to the removal of some xenobiotics in the environment. The technique has been used in the removal of radioactive ions such as cesium-137 from nuclear waste and aromatic amines derived from the cosmetic industry. -Example #2: Biodegradable Substances Substances that cannot be broken down by natural processes, which mostly involve microbial action, are said to be non-biodegradable. Often contain Carbon-Halogen bonds or aromatic structures. On the other hand, a compound is biodegradable if it can undergo bacterial degradation into end products that are found in nature, and therefore are not harmful to the environment. i. Plant-based hydro-biodegradable plastic This plastic has a high starch content, and is often obtained from corn. Genetic modification of grasses may help to produce similar plastics. The breakdown is initiated by hydrolysis and produces carbon dioxide and water. Swelling of starch grains can help to break up the plastic. ii. Petroleum-based oxo-biodegradable plastic This is derived from a by-product of the oil industry. Additives, often cobalt, are used to act as catalysts for the breakdown process, which can be programmed for different times depending on the use of the plastic. The plastic degrades into microfragments which are dispersed and eventually broken down by bacteria. Can be composted with natural food products. -Example #3: Bioremediation – the use of enzymes Although as a fossil fuel, crude oil is a natural product, it can be present in sufficient concentrations to be considered xenobiotic. (ie. During an oil spill) Ways to ameliorate the impact of oil spills include the use of microorganisms which are able to break the oil down by using it as a food source and oxidize it in respiration. This is known as bioremediation.

- Green Chemistry -Also known as sustainable chemistry

-Green Chemistry - Examples - Food and Drink Carbon dioxide under pressure is known as supercritical carbon dioxide, and can penetrate into substances and act as a solvent. It is cheap and non-toxic. It is used in the extraction of caffeine in the preparation of decaffeinated coffee, replacing previously used toxic solvents. It is also used to remove fungicide contaminants from wine-bottlecorks, and to pull pungent oil out of sesame seeds.

2. Bioplastics Plastics derived from corn starch which has been converted into a resin by bacteria can replace traditional oil-based plastics. Genetically engineered plants such as tobacco may be able to harvest useable plastics.

3. Cosmetics Production of esters for face creams has traditionally used sulfuric acid at high temperatures, but can be done using enzymes at room temperature. 4. Clothing Industry Enzymes can replace polluting detergents and improve energy efficiency by enabling effective cleaning at lower temperatures. Renewably sourced textile fibres such as bamboo and eucalyptus may replace synthetic materials from the petrochemical industry or fabrics such as cotton which rely on heavy use of fertilizers. B.7 - Enzymes -Enzymes are biological catalysts. -Enzymes increase rate of reaction by providing an alternate pathway with lower activation energy. -They are responsible for thousands of metabolic processes in living orgnisms. -Describe the characteristics of biological catalysts (enzymes) Enzymes are proteins (mostly) Highly specific for their substrates Work in narrow pH range and temperature Enzyme activity depends on their tertiary and quaternary structure. Work by either lock and key mechanism or by induced fit model (enzymes change shape to fit shape of substrate) -Compare inorganic catalysts and biological catalysts (enzymes)

Inorganic catalysts : Mineral ions/ Simple inorganic molecules Can catalyze several different reactions Wider range, less sensitive to PH or temperature changes Increases rates by fractions Are not regulated by other molecules Are not synthesized in living cells Biological Catalyst : Globular proteins (complex organic molecules) Can catalyze several different reactions Catalyze specific types of reactions (substrate specific) Narrow pH and temperature range Increase rates by fractions Increase rates by 10^3-10^6 Are regulated by specific molecules (cofactors) Are synthesized in living cells by ribosomes Increase rate of reaction by lowering activation energy - Describe the relationship between substrate concentration and enzyme activity - At low [S] (substrate conc.) rate of reaction is proportional to [S], 1st order,as there are active sites available for binding. - As [S] further increases, rate increase slows down and eventually stops, due to occupation of active sites. -At very high [S], rate is constant (max rate), 0th reaction order (unaffected), because all enzymes are saturated with substrates. -Determine Vmax and the value of Michaelis constant (Km) by graphical means and explain its significance - Vmax: maximum rate of reaction, when enzyme is saturated with substrate - Km: is the concentration of substrate which permits the enzyme to achieve half Vmax. (experimentally determined) The higher Km, the lower enzyme's activity. -Importance of determining Km The Km of an enzyme, relative to the concentration of its substrate under normal conditions permits prediction of whether or not the rate of formation of product will be affected by the availability of substrate. -An enzyme with a low Km relative to the physiological concentration of substrate, is normally saturated with substrate, and will act at a more or less constant rate, regardless of variations in the concentration of substrate within the physiological range. -An enzyme with a high Km relative to the physiological concentration of substrate, as shown above, is not normally saturated with substrate and its activity will vary as the concentration of substrate varies, so that the rate of formation of product will depend on the availability of substrate. -If two enzymes, in different pathways, compete for the same substrate, then knowing the values of Km and Vmax for both enzymes permits prediction of the metabolic fate of the substrate and the relative amount that will flow through each pathway under various conditions.

-Describe the mechanism of enzyme action, including enzyme substrate complex, active site and induced fit model GENERAL PRINCIPLE : 1. Substrate binds to active site of enzyme 2. Enzyme-substrate complex forms 3. Products + unchanged enzyme -Compare competitive inhibition and non-competitive inhibition -Inhibitor: chemical that prevents substrate binding to enzyme; deactivates enzyme. Competitve: when a inhibitor chemically resembles substrate and therefore can bind to enzyme's active site instead of substrate. - Non-competitive: compound binds to other site than active site what alters the shape of active site thus preventing the binding between substrate and enzyme. -State and explain the effects of heavy-metal ions, temperature changes and pH changes on enzyme activity - Heavy metal ions: React irreversibly with -SH group by replacing H atom and forming a covalent bond between S atom and the heavy metal ion Ion poisons enzyme by binding to active site Ion disrupts folding of enzyme, structure alterations ->> Lead to stuctural changes, reduction in activity Heavy metal examples: mercury, chromium, thalium, lead, zink, nickel. -Temperature changes: Increacing temperature increases rate of enzymatic reaction, i.e. product formation, until a certain point. According to collision theory, increased temperatures result in more frequent collisions between enzyme and substrate. Rate of reacion drops sharply when certain denaturation temperature is reached, i.e. enzyme disintegrates, since hydrogen and other non-covalent bonds are broken. -pH changes At narrow pH range, enzyme is active. Deviations from optimum pH cause denaturation of enzyme. B.8 Nucleic Acids Understandings:

* Nucleotides are the condensation products of a pentose sugar, phosphoric acid and a nitrogenous base. * Polynucleotides form by condensation reactions. * DNA is a double helix of two polynucleotide strands held together by hydrogen bonds. * RNA is usually a single polynucleotide chain that contains uracil in place of thymine and the sugar ribose in place of deoxyribose. * The sequence of bases in DNA determines the primary structure of proteins synthesized by the cell using a triplet code, known as the genetic code, which is universal. * Genetically modified organisms have genetic material that has been altered by genetic engineering, involving transferring DNA between species. Heredity and the Storage of Biological Information: * Thousands of proteins with strictly defined structures and functions exist in all organisms. * Cells of an organism share similar amino acid sequences of specific proteins, which only slightly differ between individuals of the same species. * A mechanism that permits cells to store and interpret biological information, and well as transfer it to other cells and organism must exist. * Heredityà Allows the passing of anatomical and biochemical characteristics of the species from generation to generation, and takes place in the nucleus of the cell. Organisms obtain some information from their parents this way. DNA as the Carrier of Genetic Information: * Not all genes can be related to specific proteins but each gene is responsible for the production of a ribonucleic acid (RNA). Nucleic Acids: * Nucleic acids are molecules that allow organisms to transfer genetic information from one generation to the next. There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). * They are condensation polymers of nucleotides, which are the products of condensation of a nitrogenous base, a pentose sugar and phosphoric acid. Nitrogenous Bases and Nucleotides * Nitrogenous bases A nitrogen containing molecule that has the same chemical properties as a base. Used in the construction of nucleotides, which in turn build up the nucleic acids like DNA and RNA. * they are heterocyclic aromatic amines that contain several nitrogen atoms and act as proton acceptors in aqueous solutions. * All common nitrogenous bases are derived from two parent amines, pyrimidine and purine. Pyrimidine Purine * Cytosine, thymine, uracil. * Cytosine in found in all nucleic acids. * Thymine is normally associated with

deoxyribose sugar and is found in deoxyribonucleic acids. * Uracil forms nucleotides with ribose and is found in ribonucleic acids. * Adenine, guanine. * Both purines are found in nucleic acids. * Both DNA and RNA include four nitrogenous bases each, including two purines and two* pyrimidines. For DNA these bases are A, G, C and T. For RNA these bases are A, G, C and U * Nitrogenous bases are crystalline substances with high melting points due to the presence of multiple polar groups. * They are predominantly. hydrophobic * Unlike amino acids, these bases are almost insoluble in water because their molecules are held together by strong hydrogen bonds. * Thymine or uracil can form two hydrogen bonds with adenine while cytosine and guanine bind to each other by three hydrogen bonds. * Complementary base pairingà Describes the manner in which the nitrogenous bases of the DNA molecules align with each other. * Adenine/thymine (A=T), adenine/uracil (A=U), guanine/cytosine (G=C) are known as complementary base pairs. * The ability of nitrogenous bases to form hydrogen bonds with one another in a specific order and orientation plays an important part in the storing and processing of genetic information. * Nucleotidesà The monomeric units of nucleic acids. * These building blocks are composed of nitrogenous bases, a pentose sugar and phosphoric acid. Adenosine Triphosphate: * Adenosine triphosphate (ATP) is often called the “molecular currency” of energy transfer, which is constantly being hydrolysed and synthesized within the body. * The human body contains 250 g of ATP, which depending on the level of physical activity gets converted into energy each day. * Some nucleotides, such as adenosine 5’-triphosphate (ATP), contain more than one phosphate group in their molecules. * When the terminal phosphate group in ATP is hydrolysed, it releases energy that can be used by other metabolic processes or transferred into mechanical work. * ATP molecules also act as coenzymes in many biological reactions. Nucleic Acids: * Living cells contain two types of nucleic acid: ribonucleic acids (RNA) and deoxyribonucleic acids (DNA). * Ribonucleic acids are condensation polymers of ribonucleotides, and contain ribose residues. * Deoxyribonucleic acids are composed of deoxynucleotides, and contain residues of deoxyribose. * When nucleotides combine with one another, the phosphate groups form diester bridges between 3’ and 5’ carbon atoms of adjacent pentose residues. * Condensation reactions produce long polynucleotide chains known as strands, in which monomeric units are joined together in strict order and orientation. * Like proteins, each DNA and RNA strand had two terminals (ends), which are called 3’ and 5’ ends.

* In living cells the synthesis or creation of nucleic acids begins from their 5’ ends. * Primary structureà In DNA and RNA the sequence of nucleotides linked together by phosphodiester covalent bonds in known as the primary structure of nucleic acid. The Structure of DNA: * DNA molecules consist of two polynucleotide strands in which each nitrogenous base from one strand forms a complementary pair with a nitrogenous base from another strand. * Each pair contains one purine base (A or G), and one pyrimidine base (T or C). * Secondary structureà The double-helix shape of the DNA molecule stabilized by hydrogen bonds between complementary nitrogenous bases is known as its secondary structure. Intermolecular Bonding Stabilizes Nucleic Acids: * At physiological pH (7.4), phosphate groups in nucleotides and nucleic acids are almost completely ionized, so the whole molecule of DNA or RNA becomes a negatively charged polyion. * The ionized phosphate groups are hydrophilic and form multiple hydrogen bonds with water molecules. * Negatively charged DNA interacts with basic chromosomal proteins and histones which are positively charged at physiological pH. * Intermolecular bonds formed by hydrophobic and hydrophilic parts of polynucleotide chains stabilize the double-helical shape of DNA and make it highly resistant to chemical cleavage. DNA Replication: * The human body contains more than one trillion cells, most of which have a very limited life spans and need to be replaced regularly. * All cells of an individual organism contain identical DNA. * DNA replication: A mechanism by which exact copies of DNA molecules are created. This process is facilitated by several enzymes, and includes three steps: initiation, elongation and termination. * The first group of enzymes, initiator proteins, separate the two DNA strands and create short polynucleotide fragments (primers) paired with the separated strands by complementary nitrogenous bases. * Another group of enzymes known as DNA polymerases add more nucleotides to the primers using the existing DNA strands as templates. * The resulting new polynucleotide chains are complementary to existing DNA strands and therefore produce two identical copies of the original DNA molecule. * The replication process is terminated either by a certain sequence in the DNA or by the action of proteins that bind to the specific DNA regions. Transcription: * Transcription A mechanism like replication, used when an RNA molecule is created from a DNA template. * During transcription, a DNA sequence is read by an RNA polymerase, which produced an RNA molecule complementary to an existing DNA strand. * The RNA molecule contains ribose sugar (instead of deoxyribose in DNA) and uracil nitrogenous base (instead of thymine in DNA).

* The new RNA molecules usually exist as single polynucleotide strands with various three-dimensional configurations. * The exact shape of an individual RNA molecule, known as its secondary structure, is determined by hydrogen bonds between complementary nitrogenous bases from different regions of the same strand. * Each type of nucleic acid plays its own role in heredity. * DNA resides in chromosomes, stores genetic information, and acts as a template from which this information is copied to RNA. * The resulting RNA molecules then transfer the genetic information from chromosomes to other regions of the cell, and can be used as templates for protein synthesis. * Translationà The process in which ribosomes in a cell's cytoplasm create proteins, following transcription of DNA to RNA in the cell's nucleus. * All living organisms use the same genetic code that allows ribosomes to translate three-nucleotide sequences (triplets, or codons) into sequences of amino acid residues in polypeptide chains. Genetic Engineering: * Genetic Engineering Refer to the detailed understanding of DNA structure and function that leads to the development of laboratory techniques for DNA manipulation. * Certain techniques allow scientists to alter DNA sequences in the genes of living organisms. * GMO (genetically modified organism)à The result of a laboratory process where genes from the DNA of one species are extracted and artificially forced into the genes of an unrelated plant or animal. * GMO’s possess advantageous qualities such as resistance to pests, viruses and herbicides, tolerance to harsh environmental conditions, higher crop yield, and increases nutritional value. * These organisms raise many ethical health and environmental issues. * The long-term effect of their consumption remains unknown. B.9 Biological Pigments Understandings: * Biological pigments are colored compounds produced by metabolism. * The colour of pigments is due to highly conjugates systems with delocalized electrons, which have intense absorption bands in the visible regions. * Porphyrins, such as hemoglobin, myoglobin, chlorophyll and cytochromes are chelates of metals with large nitrogen-containing macrocyclic ligands. * Hemoglobin and myoglobin contain heme groups with the porphyrin group bound to an iron (II) ion. * Cytochromes contain heme groups in which the iron interconverts between iron (II) and iron (III) during redox reactions. * Anthocyanins are aromatic, water-soluble pigments widely distributed in plants. Their specific colour depends on metal ions and pH. * Carotenes are lipid-soluble pigments, and are involved in harvesting light in photosynthesis. They are susceptible to oxidation, catalyzed by light.

Coloured Compounds: * Most organic compounds are colourless because they do not absorb electromagnetic radiation in the visible range of the spectrum. * Electron transitions in such compounds require relatively high energy, which corresponds to ultraviolet (UV) light and cannot be detected by the human eye. * The presence of multi-centre chemical bonds and electron conjugation lowers the energy of electron transitions and therefore increases the wavelength of absorbed radiation. * Molecules with many delocalized electrons absorb visible light and appear coloured. Carotenes: * Biological pigments Coloured compounds produced in living organisms, containing molecules with extensive systems of alternate single and double carbon-carbon bonds. * the p-electron clouds of adjacent double bonds overlap and produce long chains of carbon-carbon bonds with delocalized electrons and an average bond order of 1.5. * The colour of a biological pigment depends on its molecular structure and on the number of delocalized electrons. * Larger conjugation systems typically absorb light of lower energy, which corresponds to lower frequency and longer wavelength. * If the wavelength at which the maximum of absorption occurs is known, the colour of the pigment can be predicted. * Carotenes and other group A vitamins are fat soluble, so they accumulate in lipid tissues and are largely responsible for the yellowish colour of animal fat. Carotenes as Antioxidants: * The ability of carotenes to absorb visible light makes these compounds very sensitive to photo-oxidation. * In living organisms carotenes and other group A vitamins act as antioxidants, protecting the cells from UV light, peroxides and free radicals, including a highly reactive “singlet oxygen” produced by photosynthesis. * Carotenes absorb some light energy that cannot be utilized by chlorophyll and increase the efficiency of the photosynthetic reactions in green plants. Porphyrins: * Porphyrins Complexes of metal ions with large cyclic ligands. * The organic backbone of porphyrins, known as porphin, contains four nitrogen atoms in a highly conjugated aromatic heterocycle. * The nitrogen atoms in porphin and porphyrins can bind to metal ions, producing very stable chelate complexes.

* Hemesà Iron complexes of porphyrins. * Hemes act as prosthetic groups in various metalloproteins, including myoglobin, hemoglobin and cytochromes. * The iron (II) ion in heme can form two additional coordination bonds: one with a histidine residue of the protein and one with an inorganic molecule such as oxygen or water. * Myoglobin and hemoglobin are responsible for the transport and release of molecular oxygen to cells so that it can be used for respiration and other metabolic processes. * Complexes of porphyrins with d-block elements absorb visible light due to electron transitions in the conjugate macrocyclic system and between d-orbitals of the metal ion. * All proteins with prosthetic heme groups are brightly coloured. * Hemoglobin is composed of four protein subunits that are structurally similar to myoglobin. Each subunit contains a heme prosthetic group that can bind one molecule of oxygen. Hemoglobin can therefore carry up to four oxygen molecules. Cooperative Binding in Hemoglobin: * Cooperative binding Occurs in binding systems containing more than one type, or species, of molecule and in which one of the partners is not mono-valent and can bind more than one molecule of the other species. * The interaction between hemoglobin and molecular oxygen is an example of cooperative binding. * According to the induced fit model, the binding of a substrate to a free active site alters the shape of the entire hemoglobin molecule, including the shapes of active sites in all four protein subunits. * These changes increase the affinity of partly oxygenated hemoglobin to molecular oxygen. * Cooperative binding increases the efficiency of oxygen transport in the human. * In arterial blood, where the partial pressure of oxygen is high, most of the binding sites in hemoglobin become occupied by oxygen molecules. * This further increases its affinity for oxygen, allowing hemoglobin to reach saturation point quickly and carry as much oxygen as possible from the lungs to other tissues. * As partial pressure of oxygen decreases some oxygen molecules are released, which reduces the affinity of hemoglobin for oxygen and accelerates the loss of remaining oxygen molecules. Other Factors Affecting the Affinity of Hemoglobin for Oxygen: * Temperature, pH, and concentration of carbon dioxide can affect the affinity of hemoglobin for oxygen. * At abnormally high body temperature the ability of hemoglobin to carry oxygen decreases due to unfavourable conformational changes of the active sites and the positive entropy of dissociation of hemoglobin-oxygen complexes. * Low body temperature increases the affinity of hemoglobin for oxygen. * Carbon dioxide acts as a competitive inhibitor that binds directly to heme prosthetic groups. * Competitive and noncompetitive inhibition facilitate the release of oxygen. Cytochromes: * Cytochromes A group of enzymes. * Molecular oxygen, which is supplied to cellular tissues by hemoglobin, is reduced to water during the final step of aerobic respiration. This takes place in the mitochondria and involves cytochromes.

Chlorophyll: * Chlorophyll A green pigment found in cyanobacteria and the chloroplasts of green plants. * The ability of chlorophyll to absorb energy from visible light is utilized by living organisms in the process of photosynthesis. * Chlorophyll in structurally similar to heme but contains a different metal ion (magnesium instead or iron) and different substituents at several positions on it porphin backbone. * Its structural backbone, chlorin, is very similar to porphin but is more reduced and contains an additional five-membered hydrocarbon ring. * Photosystemsà A collective group of proteins and pigments involved in photosynthesis. The Absorption Spectrum of Chlorophyll: * Chlorophyll absorbs electromagnetic radiation in the blue and red regions of the visible spectrum. At the same time, green and near-green portions of the spectrum are reflected or transmitted, which is responsible for the green colour of plant leaves and other chlorophyll-containing tissues. Anthocyanins: * Anthocyanins A group of biological pigments that are responsible for the bright colours in living organisms such as plants, fruits and vegetables. * All anthocyanins are water soluble and concentrate in the vacuoles of plant cells, producing characteristic red, purple and blue colours of chlorophyll-free plant tissues. * Anthocyanins are tricyclic polyphenols with an aromatic backbone (flavylium ion) and several substituents including a residue of a-glucose. Color Changes in Anthocyanins * The exact colors of anthocyanins in solution depend on the presence of metal ions and the solution pH. * Metal ions such as Mg2+ and Fe3+ form stable complexes with anthocyanins, which are responsible for the colours of flower petals. * In the absence of metals the colours of most anthocyanins change from red in acidic solutions to purple in neutral and blue in slightly alkaline solutions. * This colour change is the result of acid-base reactions that involve the aromatic backbone of anthocyanins and affect the degree of electron conjugation in their molecules or ions. * In acidic solutions, anthocyanins exist as protonated flavylium cations. As the acidity decreases these cations lose one or two protons, producing neutral quinoidal bases or phenolate anions. * The loss of protons increases the electron density in the aromatic backbone and lowers the energy of electron transitions. * The wavelength of the absorbed light increases and the maximum of absorption shifts from the green visible spectrum, to yellow, and finally to orange. * The actual colours of anthocyanins at different pH are complementary to their absorption maxima.

* Because anthocyanins are pH sensitive, and absorb visible light, they can be used as natural acid-base indicators and organic components of dye-sensitive solar cells. * The bright colours of flowers and fruits produce by anthocyanins attract insects and animals that provide pollination and seed dispersal. * In green leaves, anthocyanins absorb certain wavelengths of visible and UV light, protecting photosynthesizing pigments and plant tissues from excessive exposure to solar radiation. * The presence of highly conjugated electron systems in anthocyanins makes them efficient antioxidants. * The ability of biological pigments to absorb light and act as free radical scavengers reduces their own stability and makes them particularly sensitive to photo-oxidation.