Outcome 4Biochemistry

Biochemical FuelsBiochemical fuels (biofuels) are fuels derived from plant materialsBiochemical fuels are carbon neutral. The plant materials used in the generation of biochemical fuels are produced by photosynthesis, which removes carbon dioxide from the atmosphere and produces glucose. The plants convert the glucose into cellulose and starch (polysaccharides). The carbon dioxide is then released when the biochemical fuel is burned.

Bioethanol Enzymes in yeast are used to convert starches and sugars to ethanol C6H12O6(aq) 2CH3CH2OH(aq) +2CO2(g) Enzymes are used to catalyse the breakdown of the polysaccharide starch in grains to glucose Then the fermentation process uses other enzymes from yeast organisms to convert small sugar molecules such a glucose to ethanol and carbon dioxide The fermentation stops when the ethanol content is between 10 and 20%, at which point the yeasts and their enzymes can no longer function The fermented mixture is pumped to an evaporation plant where steam is added to cause the (lower boiling point) ethanol to evaporate off This is dehydrated (water is removed) leaving ethanol that is 99.7% pure In Australia, the final ethanol is then denatured (poisoned) by adding up to 5% petrol to make it unsuitable for consumption Wastes: The carbon dioxide produced in the fermentation step can be sold to soft drink manufacturers, the waste water can be used for irrigating crop and the remains from the fermentation can be sold as animal feed

BiodieselBiodiesel is a mix of esters produced by a chemical reaction between vegetable oil and an alcohol Fats and oils are tryglycerides with a molecular structure consisting of three hydrocarbon chains attached by ester functional groups to a backbone of three carbon atoms The triglyceride is hydrolysed by warming it with methanol and potassium hydroxide solution. The potassium hydroxide solution acts as a catalyst in this hydrolysis reaction so that overall the triglyceride breaks down to three molecules of fatty acid esters, plus glycerolBiogasBiogas consists mainly of carbon dioxide and methane in roughly equal quantities and is generated when organic material decays in the absence of oxygen

FatsA fat is a name used to describe a large number of organic compounds belonging to an even larger class of biological molecules called lipids. Lipids include fats, oils, waxes and steroids. They also contain small amounts of oxygen and, occasionally, other elements. Most lipids are essentially non-polar and so they are insoluble in waterFats and oils have very similar chemical structures. They are distinguished on the basis of their physical states at normal temperatures, fats are solids and oils are liquids.Most fats and oils (triglycerides) are formed by a condensation reaction between a single molecule of glycerol and three molecules of fatty acids.Triglycerides are large, non-polar molecules and therefore insoluble in aqueous solution

Types of fatsFats are distinguished on the basis of the fatty acids from which they are made Saturated fats are made from fatty acids, that contain only single carbon-carbon bonds Mono-unsaturated fats are made from fatty acids that contain one carbon-carbon double bond Polyunsaturated fats are made from fatty acids that contain more than one carbon-carbon double bond. Polyunsaturated fats have lower melting points than unsaturated fats, and often occur as liquids (oils) at room temperature. They are more reactive than saturated fats.The different physical states of saturated and polyunsaturated fats are thought to arise because molecules of saturated fats can pack more closely together, resulting in stronger dispersion forces between the molecules.The arrangement of the carbon chain section at the double bonds sites of polyunsaturated fats do not permit such close packing. Consequently saturated fats have higher melting points than unsaturated fats

Reactions of fats Hydrolysis/condensation Hydrogenation: Many fats and oils are unsaturated, we use the process of hardening to make solid fats from liquid oils. The more saturated the fat, the higher the melting point

Digestion of fats The enzyme pancreatic lipase splits fats molecules into fatty acids and glycerol in the duodenum This enzyme requires the action of bile salts which is secreted by the liver The bile acts as an emulsifying agent and breaks the fats into smaller droplets with become suspended in water

Absorption of fats The fatty acids diffuse into the blood vessels of the small intestines where they are reassembled into triglycerides They are then converted into lipoproteins for transport around the body In the liver the lipoproteins are converted back into a triglycerides and stored When needed as an energy source their triglycerides are hydrolysed to free their fatty acids The fatty acids then travel to the cells and are then oxidized to produce energy

Condensation PolymerisationThe monomers used to make a polymer by a condensation polymerization reaction have a pair of functional groups that are able to react together, producing a new functional group that links the monomers and also producing a small molecule such as water. Features of monomers (functional group in monomers) used to produce different types of polymers:Polyester Carboxyl (-COOH) and hydroxyl (-OH)Polyamide (polypeptide)Carboxyl (-COOH) and amine (-NH2)PolysaccharideHydroxyl (-OH) and hydroxyl (-OH)

CarbohydratesCarbohydrates are made from the elements carbon, hydrogen and oxygen, and usually have the formula Cx(H2O)y where x and y are whole numbers. Monosaccharides The smallest carbohydrates are the monosaccharides White crystalline solids Highly soluble in water Sugars (Sweet taste) E.g. C6H12O6: Glucose, Fructose, Galactose Above three molecules contain a number of polar OH groups, enabling them to form hydrogen bonds with water highly soluble in waterDisaccharides The carbohydrate formed when two monosaccharides undergo a condensation reaction The hydroxyl functional groups react to form the disaccharide and water The two rings are joined via an oxygen atom. This linkage is called a glycosidic (or ether) linkage E.g. Maltose (Glucose+Glucose), Sucrose (Glucose+Fructose) and Lactose (Glucose + Galactose)Polysaccharides Polymer carbohydrates made by linking monosaccharides into a chain Polymers of glucose molecules linked together by condensation reactions E.g. Glycogen, starch and cellulose

ProteinsProteins are found in every cell and are fundamental to cell structure and operation

Amino acids Proteins are polymers built up from small monomer molecules called amino acids Every amino acid has an amino group (NH2) and a carboxyl group (COOH) General formula H2N-CHZ-COOH The major difference between one amino acid and another is the collection of atoms that make up the side chain known as the Z group. These amino acids are known as 2-amino acids or -amino acids because the amino, carboxyl and Z groups are all attached to the second carbon atom As a consequence of the polar amino and carboxyl functional groups, amino acids are soluble in water The amino group can act as a base and the carboxyl group can act as an acid. Thus an amino acid molecule in a solution at a particular pH will usually be in the form +H3N-CHZ-COO-. Such as molecule is called a zwitterion or dipolar ion. A proton has been lost from the acidic carboxyl group and the basic amino group has gained a proton. The dual acidic and basic nature of amino acids means that several different forms of an amino acid can be in equilibrium in a solution:+H3N-CHZ-COO-(aq) + H3O+(aq) +H3N-CHZ-COOH(aq) + H2O(l)+H3N-CHZ-COO-(aq) + OH-(aq) H2N-CHZ-COO-(aq) + H2O(l) In acidic solutions the +H3N-CHZ-COOH form is most abundant, whereas the H2N-CHZ-COO- form is most abundant in alkaline solutions

Protein structureProteins are polymers formed by a condensation reaction between a carboxyl group COOH and an amine group NH2, where an amide function group or peptide linkage CONH- that links the two molecules is formed. A covalent bond is formed and a water molecule is eliminated.Molecules made from amino acids are often called peptides. When two amino acid molecules react together a dipeptide is formed, and when three molecules react together a tripeptide is formed. A polymer made from amino acids is known as a polypeptide, and polypeptides built up from more than 50 amino acids are usually called proteins.The role that any protein fulfills in an organism depends on its shape.

Primary Structure A sequence of amino acids The order of the amino acids is known as the proteins primary structure The entire shape of a protein is a consequence of the precise order in which its amino acids are joined together

Secondary Structure Parts of the chain can attract each other (hydrogen bonding), creating particular three-dimensional shapes Coiling, folding or pleating of sections of a protein is described as the proteins secondary structure

Tertiary Structure The Z groups in the amino acid units of a protein molecule influence the overall three-dimensional shape of the molecule. Some of these side groups are capable of forming bonds with side groups elsewhere on the protein chain Hydrogen bonds between polar Z groups (between OH or NH groups) Ionic interactions between a Z group (between NH3+ and another group that contains COO-) Covalent cross-links between chains, particularly where the amino acid cysteine (containing an SH group) is present. Two neighbouring chains with cysteine units can react, forming a disulfide link (-S-S-). Disulfide bridges are found in many proteins, including insulin Dispersion forces between non-polar Z groups (e.g. valine and phenylalanine)

Enzymes: biological catalystsThe biological catalysts that accelerate the rate of chemical reactions in living things are a type of protein called enzymesCompared to inorganic catalysts: Enzymes produce much faster reaction rates Enzymes operate under much milder conditions Enzymes are more sensitive Enzymes are very selectiveThe catalytic activity of an enzyme depends on its tertiary structure. The active site of an enzyme is usually a flexible hollow or cavity within the molecule. Some enzymes have small, non-protein parts called cofactors, such as vitamins or metal atoms, associated with the active site. These cofactors are necessary for catalytic effect.A reactant molecule, known as the substrate, is maneuvered into this site and it is there at the surface of the enzyme that reaction takes place.The steps in the action of an enzyme are as follows:1. The reactant (substrate) enters the active site2. Bonds formed between the enzyme and substrate weaken bonds within the substrate, lowering the reactions activation energy3. The substrate breaks or rearranges into new products and these products are releasedIn many cases, the enzyme and substrate bind together because part of the substrate and the active site are non-polar and so dispersion forces are significant. In other cases, the substrate is held in place by attraction between positive and negative charges, attraction of a metal ion in the enzyme to a negative dipole on the substrate, or hydrogen bonding between enzyme and substrate.Some types of bonds that can for between enzyme and substrate: Ion-dipole interactions (between Zn2+ and O=C) Hydrogen bonds (between N-H and O=C) Ionic interactions (O- and +NH3)Denaturation of enzymesA change that destroys the biological activity of a protein is called denaturation. Denaturation may result because of increased temperature, a change in pH, or the addition of various chemicals.Once a protein has been denatured, the unfolded chains tend to form randomly looped structures which dome into close contact. The chains become entangled and bond with each other, often by disulfide bridges, so that large clumps of protein molecules are formed. This process is called coagulation.

DNAThe Structure of DNA DNA is a condensation polymer constructed from four different monomers known as nucleotides Each nucleotide consists of a phosphate group deoxyribose sugar molecule one of the four bases; adenine (A), cytosine (C), guanine (G) and thymine (T) The complementary base pairs adenine and guanine are referred to as purine bases and cytosine and thymine are referred to as pyrimidine bases

Formation of a nucleotide The base forms a covalent bond to the carbon atom labeled C1 in the deoxyribose molecule The phosphate group bonds to the carbon atom labeled C5 in the deoxyribose molecule A water molecule is produced when each bond is formed

Primary structure of DNA Covalent bonds are responsible for producing the primary structure of DNA A covalent bond is formed between the 5- phosphate group on one nucleotide and the 3- hydroxyl group on the deoxyribose of another nucleotide The end of the DNA strand with the phosphate group is called the 5 end and the end with the hydroxyl group is called the 3 end

Secondary structure of DNA The secondary structure of DNA is a pair of DNA polynucleotide strands held together by hydrogen bonding between the bases adenine-thymine and cytosine-guanine Two hydrogen bonds can form between the bases adenine and thymine Three hydrogen bonds can form between the bases cytosine and guanine The structure twists around to form an antiparallel double helix the shape of a spiral staircase where the sugar-phosphate backbone forms the handrails and the pair of bases are the steps

Tertiary structure of DNA The phosphate groups in the backbone of the double helix give DNA a negative charge, and this enables DNA molecules to interact with a group of proteins called histones, which are positively charged The DNA molecules wrap around histones and become coiled. This allows the DNA to be very tightly and efficiently packaged with each molecule forming a structure known as a chromosome

AspirinA drug is defined as any substance that alters a chemical process in the body Aspirin can be produced by reacting ethanoic acid with salicylic acid. This is a slow reaction, the yield is low and the water produced drives the reaction backwards An alternative reaction pathway is to produce ethanoic anhydride from ethanoic acid. This is then reacted with salicylic acid to produce acetylsalicylic acid (aspirin)Pure acetylsalicylic acid is not very soluble in water despite the presence of COOH functional group. Converting the COOH functional group in the sodium salt changes the molecule into an ion and makes it more soluble

Polyaspirin A recent development is to make a polymer structure using a condensation reaction between salicylic acid and 1,8-octanedioic acid This larger molecule passes through the stomach to the small intestine, where it enters the bloodstream before it is hydrolysed to salicylic acid. This means it doesnt irritate the stomach