Chemical Bonds for Biology Workbook PDF

Workbook Name _______________ Set ____ An introduction to the chemistry behind biomolecules What is biochemistry? Well, it’s the study of biology at a molecular level. So the emphasis of this unit is the biol...

Workbook Name _______________ Set ____ An introduction to the chemistry behind biomolecules What is biochemistry? Well, it’s the study of biology at a molecular level. So the emphasis of this unit is the biological significance of chemical molecules. As part of the course, there are six biological molecules that you need to know about: CH2OH Carbohydrates H O H These molecules are one of many vital to life. They are used for energy (for both storing and supplying energy), and in some cases can be used structurally, such as cellulose OH OH H Lipids O H C O C H O H C O C These come in many varieties: fats, oils, cholesterol, steroids, H and more, and have uses in cellular membranes, insulating O and protecting, and also act as a minor energy supply H C O C H H Proteins Proteins have several uses, such as for transport and structure; but they are also the basic components of all enzymes, hormones, antibodies, haemoglobin, ribosomes, and many more materials Water H Another essential life component, this is the most important O content of many reactions forming most of these molecules, and also metabolic reactions; water is also an essential H structural component in plants, and in the diet of animals Nucleic acids These are responsible for the formation of both DNA and all forms of RNA molecules, consisting of individual nucleotides  Enzymes These are proteins which are used in many reactions – their function is to catalyse metabolic reactions in the vast majority of living organisms There is a lot of chemistry knowledge in the Biological Molecules section of this module, which is why it is important that you are aware of a few chemistry basics, such as the types of chemical bond. This unit on Biological Molecules is centred around organic chemistry (organic being ‘involving carbon’). All of the molecules studied are carbon-based, with the exception of water, which only contains the elements hydrogen and oxygen. Covalent bonds As you may well know from GCSE chemistry, a stable atom is one with a completed outer H H energy level (shell). For the majority of elements, this number is eight, which goes for carbon too. Carbon, however, naturally has four electrons in its outer energy level: so to stabilise it C must share four electrons with other atoms, which forms covalent bonds. So it can form four H covalent bonds – and these can be with other carbon atoms, or other atom types. H Double bonds These types of covalent bond also exist, where atoms share multiple electrons in order to stabilise where there is a lack of available atoms. Common examples of the double H bond are found within carbon and oxygen atoms (the carbon C=C double bond and the carbon-oxygen C=O double bond). H C H C Ionic bonds H An ionic bond occurs between two oppositely charged ions. This will always take place between a metal and a non-metal ion. This involves the donation of electrons from the outer energy level, rather than the sharing which happens in covalent bonds. The metal ion will donate one or multiple electrons to the non-metal, which causes the metal to Na+ become positively charged (due to the loss of a negative electron) and the non-metal to Cl- become negatively charged. The two polar ions then are brought together due to the opposite charges. These bonds are much weaker than covalent bonds. Hydrogen bonds δ + This is possibly the most important type of bond studied in this unit. It is found in H just about every molecule you could think of. Hydrogen bonds are used to hold together individual monomers into large groups, called polymers. They form where O - δ a slightly positively charged part of a molecule meets a slightly negatively charged + δ part of another molecule. We use the denotation of δ to represent H δ + + δ - - electronegativity, where δ denotes a slight negative charge, and δ denotes a slight H H positive charge. These bonds are extremely weak, often describe merely as “interactions” – but when thousands of these bonds form in a polymer to hold the structure together, they are enough to stabilise a large polymerised structure. O δ -  Chemical Bonding in Biological Molecules The contents of this Factsheet are directed towards AS level By adding more alpha-glucose molecules on at positions X and Y the candidates. By studying this factsheet students should gain a backbone molecules of starch( alpha-amylose) and glycogen may be built knowledge and understanding of: up. Alpha-amylose can be between 300 and 3000 alpha-glucoses long. The other component of starch is amylopectin. This is similar to alpha-amylose glycosidic bonds in carbohydrate structure. but is branched about every twentieth glucose by a 1,6 glycosidic branch peptide bonds in polypeptide structure. link. Glycogen has a structure similar to amylopectin but branches more ester bonds in lipid structure. frequently at about every twelfth glucose. hydrogen bonding. sulphur bonding. The reactive – OH group on carbon 1, labelled Y, is a reducing group and so phosphate bonding. gives the glucose reducing properties. (the power to donate hydrogen or electrons to other substances). In alpha-glucose this group is below the ring Introduction structure and during polymerisation forms 1,4 alpha-glycosidic bonds. Glycosidic, peptide and ester bonds are formed by a process called These can be hydrolysed by alpha-amylase enzymes, for example, salivary condensation. This is the joining of molecules by the removal of water and and pancreatic amylases in mammals and diastase in seeds, and so molecules involves removing a hydroxide group from one of the molecules and a such as starch and glycogen can be digested to maltose and then by maltase hydrogen from the other molecule. This type of reaction is important in enzyme to glucose. The structures of alpha-amylose and amylopectin are synthetic processes. The reverse process, involved in digestion, is hydrolysis shown in Fig 2. which is the splitting of molecules by the addition of water. Exam Hint - Candidates will be expected to recognise and name Glycosidic bonds molecules and bonds but will not be expected to write down structural These are the bonds which join single sugars (monosaccharides) together to formulae from memory. Candidates may be asked direct questions form double sugars (disaccharides) and multiple sugars (polysaccharides). about types of bonds, or may need to refer to the different bond types The formation of a glycosidic link is shown in Fig 1. in essay answers. Fig 1. Formation of a glycosidic link carbon 1 carbon 4 CH2OH CH2OH CH2OH CH2OH H C O C O H H H C O C O hydrolysis H H H H H H C C C C + H2O H H OH H OH H C C C C OH H OH H HO O OH C C C C HO C C OH + HO C C OH condensation H OH H OH H OH H OH X alpha-maltose Y alpha-glucose alpha glucose 1,4 alpha-glycosidic link Fig 2. Structure of alpha-amylose and anmylopectin α - amylose O O O O O O O O O O O 1,4 glycosidic α - link O O O amylopectin O O O O 1,6 glycosidic branch link CH2 O O O O O O O O O O O 1 Chemical bonding in biological molecules Bio Factsheet Enzymes for breaking down the 1,6 glycosidic branch links are not present Fig 4. Formation of a peptide bond in most animals and so amylopectin (and glycogen) can only be digested by amylases down to the branch points. This leaves an indigestible residue of H H O H amylopectin, which is called dextrin. Cooking will hydrolyse the 1,6 glycosidic links and thus cooked starch can be completely digested. H2 N C C OH + N C COOH H R R In beta-glucose the reducing –OH group lies above the ring structure and when glycosidic bonds form they are 1,4 beta-glycosidic bonds (links). These are found in the structural compound, cellulose. The formation of a hydrolysis condensation beta-link is shown in Fig 3. digestion synthesis Fig 3. Formation of a 1,4 beta-glycosidic link R = rest of the molecule H 2O or the side chain + CH2OH H O H H β -glucoses C O dipeptide H OH H 2N C C N C COOH CH2OH H C C B R R C OH H H C O OH + HO C C H peptide bond H C C H OH H OH More amino acids can attach by condensation onto the amine group at B HO C C H condensation and the acid group at C so that a long chain of amino acids (a polypeptide) synthesis can be assembled. Polypeptides may be folded and cross-bonded into H OH hydrolysis particular three dimensional shapes and assembled together into proteins. CH2OH A digestion This involves hydrogen and sulphur bonds (described below) rather than C O peptide bonds. Ionic attractions may also be important in stabilising the H OH three dimensional shapes of proteins. This is illustrated in Fig 5. CH2OH H C C H2O + OH H Fig 5. Ionic association (attraction) between two parts of a C O H O C C H polypeptide chain. H C C H OH OH H HO C C H Cellobiose polypeptide chain COO- attraction between A H OH ionised acid amine groups 1,4 glycosdic beta link NH 2 + More beta glucoses can be added, on by condensation, to the disaccharide cellobiose at points A to build up a long unbranched cellulose molecule. Cellulose molecules run together in parallel fashion to form cellulose fibrils. Within a fibril the adjacent cellulose molecules cross link by hydrogen Formation of ester bonds in lipid structure bonds. (Hydrogen bonds are described below). Individually such bonds An ester bond is formed by condensation between an acid and an alcohol. are weak but their presence in large numbers gives strength which makes The main alcohol involved in lipid structure is glycerol (which has 3 alcohol cellulose a good structural material in plant cell walls. or –OH groups) and the acids involved are fatty acids. Fig 6 shows the formation of a triglyceride. Very few animals possess cellulase enzymes capable of hydrolysing beta glycosidic links and so cellulose is usually indigestible. Many fungi and Fig 6. Formation of a triglyceride bacteria possess cellulases and are important in breaking cellulose down in rotting vegetation in the soil. The microbes in the rumens of cow and sheep also possess cellulases and so can break down the cellulose in the grass that CH2OH + HOOC.R CH2O C.R condensation/ these animals eat. synthesis O Formation of peptide bonds CHOH + HOOC.R CHO C.R + 3H2O Peptide bonds are formed by condensation between the acid group of one hydrolysis/ O amino acid and the amine group of another amino acid. They enable amino digestion acids to be joined into long chains called polypeptides. Fig 4. shows the CH2OH + HOOC.R CH2O C.R formation of a dipeptide from two amino acids. O ester bond glycerol fatty acids triglyceride water R = rest of the molecule or the side chain 2 Chemical bonding in biological molecules Bio Factsheet Hydrogen bonding Sulphur bonds Water consists of two hydrogen atoms, each of which shares an electron Amino acids such as cysteine and methionine contain sulphydryl (-SH) with the single oxygen atom. These shared electrons (negative) lie closer to groups. The group has reducing properties since the H atom can be fairly the oxygen than to the hydrogens (positive protons) and so the molecule easily removed. In proteins two nearby –SH groups may become oxidised becomes a charged dipole, with two partial positive charges at one end and (hydrogen lossed) forming a cross-linking sulphur bond (–S-S-). a partial negative charge at the other end. This is shown in Fig 7. Sulphur bonds are stronger and more heat stable than hydrogen bonds and Fig 7. The water molecule so proteins that contain many sulphur bonds tend to have good stability. The RNA splitting enzyme, ribonuclease, for example, does not denature (break down) unless temperatures are raised to around 95 oC whereas most δ- proteins denature above 42 oC..... shared electron O pairs partial charges 104.5o Phosphate bonds δ+ δ+ These are found joining the adjacent nucleotides in DNA and RNA H H structure. They are formed by condensations of orthophosphoric acid (H3PO4) between the –OH groups on carbon 3 of one pentose sugar and carbon 5 of the pentose sugar of the next nucleotide. This is illustrated in Because of these charges the hydrogen atoms of one water molecule are Fig 10. attracted to the oxygen atoms of adjacent water molecules. These attractions are called hydrogen bonds and are shown in Fig 8. Fig 10. Orthophosphoric acid and a phosphate bond in RNA Fig 8. Hydrogen bonding between water molecules. HO P O RNA OH OH 2C CH2O - base H O H HO P O C C O H H H OH H OH hydrogen bonding O C C orthophosphoric carbon 3 H acid OH O O H H H H O phosphate bond HO P O carbon 5 O OH2C O CH2O - base H H C C ribose sugar H H H OH Hydrogen bonds occur between: C C parallel cellulose molecules holding them together in fibrils, OH O opposite purine and pyrimidine bases holding DNA structure together polypeptide chains holding shape and protein structure together. HO P O Fig 9 shows hydrogen bonds between nearby peptide bonds between two polypeptides. Fig 9. Hydrogen bonding in polypeptides Exam Hint – Although examiners will not expect you to be able to write down structural formulae from memory, you will be expected to R recognise molecular structures and to be able to manipulate molecules R R 1 by joining them together with appropriate bonding. C N C C N C C N C C N O H H O H H O H H O δ- H δ+ partial charges attract H O H H O H H O H H δ+ O δ- N C C N C C N C C N C 1 R R R peptide bond 1 polypeptide chains The dotted lines represent hydrogen bonds 3 Chemical bonding in biological molecules Bio Factsheet Practice Questions 1. The table below refers to some biological molecules and to the type of Answers chemical bonds they contain. Complete the table by filling in the empty boxes. Some boxes may have more than one answer. Molecule Type of bond only 1,4 alpha-glycosidic between nucleotides in nucleic acids in amylopectin ester bonds peptide bonds between polypeptide chains in glycogen 12 2. (a) Distinguish ‘condensation’ from ‘hydrolysis’. 2 (b) The diagram below shows the general structure of two molecules of amino acid. Show how they would combine to form a dipeptide. 3 H R O H R O N C C N C C H H OH H H OH (c) (i) What is the name of the bond which joins together two adjacent amino acids? 1 (ii) Name three other types of bond involved in protein structure. 3 3. The carbohydrate below has been formed from two glucose molecules. C O C O C C C C O C C C C (a) What is this type of carbohydrate called? 1 (b) What is the name of the chemical bond which joins these two hexose units together? 2 (c) What is the chemical reaction in which one or more hexose units are joined together? 1 (d) (i) Draw a diagram to show how the two glucose molecules would have been bonded when forming part of a cellulose fibril. 1 (ii) Name the type of bond involved. 1 4 Summary of Structures and Bonding Ionic Materials Simple molecular Giant covalent Metals Polymers Nanomaterials Covalent lattices Materials Metals joined to non Non metal atoms Giant covalent crystals Metal atoms joined to Very long chain New materials on the metals e.g. sodium joined to non metals like diamond, graphite metal atoms – A GIANT molecules made from by scale of 1-100nm chloride, – A GIANT e.g.Water, H2O, and sand (SiO2). A STRUCTURE joining lots of sub-units (billionths of a metre). STRUCTURE methane, CH4, Carbon GIANT STRUCTURE (monomers) – held This means they’re dioxide CO2 together by covalent made up of a few bonds hundred atoms Metal atoms transfer Two atoms overlap The positive full shell In thermosoftening Have strange electrons to non metal their outer shells and “centres” of metal atoms (thermoplastic) polymers properties, e.g. atoms to get noble gas share a pair of (which will have noble the forces between the extremely good electron electrons. This way gas arrangemnets) make chains are weak, in conductors, or good as arrangements. The they get to have filled a giant lattice. They’re thermoset polymers there catalysts because they charged ions have outer electron shells held together because are covalent cross links have a very large opposite charges and like noble gases. The they’re attracted to the between the chains that surface area. are strongly attracted covalent bonds inside sea of delocalised stop them from sliding or to each other the molecules are very electrons changing shape strong Strong forces between There are only weak Held together by lots of Strong attractions Thermosoftening Used for things like opposite charged ions forces between the strong covalent bonds, so between +ve ions and polymers get soft and paints, catalysts in so high melting and molecules, so low high melting and boiling electrons so high melting mouldable when warmed, industry, sunscreens in boiling points. melting and boiling points. Diamond very points. thermoset polymers don’t tanning lotions. High If the charges can points. There are no hard - lots of strong Delocalised electrons change shape, but will strength materials. move (e.g. when charges, so they do not bonds. Graphite soft free to move so conduct decompose if heated. They may have health dissolved or molten), conduct electricity (lubricant)(weak forces electricity and heat New, smart polymers dangers because they then ionic materials between layers, so they Layers of atoms can slide have properties like can get into our living conduct electricity can slide over each over each other, so conducting, sensitivity to cells more easily than other) Graphite conducts metals can be bent and light, light emitting,- you larger particles. electricity one delocalised shaped easily name it, they can do it! electron per carbon atom can flow between layers)