Pathways to biomolecules

1. Pathways to biomolecules Chapter 12

2. Biomolecules • Biomolecules are molecules such as fats and oils, carbohydrates, proteins and nucleic acids that are found in all living things. • They have an essential role in: • The supply of energy to the body • The growth and repair of organs and tissues • The movement of muscles • The activity of nervous and hormonal systems • The elimination of waste. • Many biomolecules are polymers.

3. Fats – Sources of fat • Humans can make most of their own fat internally. • This is usually not necessary as there is enough fat available in our diets. • Typically fat makes up about a fifth of the solid matter in the food we eat.

4. What are fats • ‘Fat’ is a name used to describe a large number of organic compounds belonging to an even larger class of biological molecules called lipids. • Fats and oils are the best known types of lipids. • The oils found in foods have quite different structures and properties from the hydrocarbon oils produced by petroleum refining. • Waxes and steroids are also members of the lipid family

5. Lipids • Lipids are based mainly on carbon and hydrogen. • They also contain small amounts of oxygen and occasionally other elements. • Most lipids are non-polar and insoluble in water. • Fats and oils are one of our sources of the non-polar vitamins A, D, E and K. • Fats and oils have very similar chemical structures, they differ because at room temp • Fats are solids • Oils are liquids

6. Production of fats • Most fats and oils are formed by a condensation reaction between a single molecule of glycerol and three molecules of fatty acids. • This produces triglycerides which are large non-polar molecules.

7. Types of Fats • Saturated fats • Contain only single C-C bonds. • Generally unreactive and occur as waxy solids at room temperature • Mono-unsaturated fats • Contain one C=C bond. • Polyunsaturated fats • Contain more than one C=C. • Lower melting point than saturated fats. • Often liquids (oils) at room temperature • They are more reactive than saturated fats.

8. Types of 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 C=C bonds in polyunsaturated fats do not permit such close packing. • Saturated fats have higher melting points than unsaturated fats.

9. What happens to fat in the body? • Chemical digestion of fat does not start until it reaches the alkaline conditions of the small intestine. • Bile breaks down the fat into smaller fat globules that increases surface area. • Secretions from the pancreas and walls of the intestine contain enzymes that hydrolise the fat into fatty acids and glycerol. • This reverses the condensation reaction. • Once absorbed into the body the fatty acids and glycerol are reassembled into fats via a condensation reaction.

10. Your Turn • Page 182 • Question 1, 2, 3

11. Carbohydrates • Made from the elements carbon, hydrogen and oxygen. • Usually have the formula Cx(H2O)y • Carbohydrates range in size from small molecules with relative molecular masses between 100 and 200 to very large polymers with molecular masses greater than one million.

12. Monosaccharides: the simple sugars • The smallest carbohydrates are monosaccharides. • They generally have a sweet taste. • They are often called sugars • Look on page 183 table 12.5 for a list of sugars

13. Glucose • The most abundant monosaccharide. • What is its molecular formula? • It is arranged in a ring. • All three of the following molecules contain a number of polar groups enabling them to form hydrogen bonds with water.

14. Disaccharides • Formed when two monosaccharides undergo a condensation reaction. • Like monosaccharides, disaccharides also dissolve in water, taste sweet and are called sugars. • Maltose is a disaccharide and is formed when two glucose molecules react with the elimination of water. • Two hydroxy functional groups react and are joined via an oxygen atom. • This linkage is called an ether(or glycosidic) linkage

16. Polysaccharides: the complex carbohydrates • Are polymer carbohydrates made by linking monosaccharides into a chain. • Polysaccharides are polymers of glucose molecules linked together in different ways by condensation reactions. • They are generally insoluble in water and have no taste. • The three most important polysaccharides biologically are: • Glycogen • Starch • cellulose.

17. Glucose storage molecules • Glycogen is the glucose storage molecule in animals • Starch is the plant equivalent. • Since glucose can be oxidised to produce energy more rapidly than fat, all animals store some glucose for use when energy is required quickly. • Excess glucose is polymerised to form glycogen, which is stored in the liver and in muscle tissue. • When no more glycogen can be stored in these places additional glucose is converted into fat.

18. Breakdown of glycogen • The polymers are first hydrolysed (catalysed by enzymes). • Every second glucose is hydrolysed to produce maltose. • Another enzyme catalyses the hydrolysis of maltose into glucose, which is absorbed into the body. • These reactions are regarded as the reverse of the condensation reactions used to form glycogen.

19. Your Turn • Page 187 • Questions 6-8

20. Types of Proteins

21. Amino Acids • Proteins are monomers built up from small monomer molecules • These monomers are called amino acids. • Have a look at Glycine and Alanine, which are two of the simpler amino acids, what do they have in common?

22. Amino Acids • There are 20 amino acids commonly found in proteins in the human body. • They are listed on pages 189-190 and in your exam data sheet. • They have the general formula • H2N-CHZ-COOH • With the Z group making up a different side chain. • These 20 amino acids are known as 2-amino acids or α-amino acids because the amino, carboxy and Z groups are all attached to the second carbon atom.

23. Amino Acids • Are soluble in water due to the polar amino and carboxy functional groups. • The amino group can act as a base and the carboxy group can act as an acid. • As a result, an amino acid molecule in a solution at a particular pH will usually be in the form: • +H2N-CHZ-COOH- • This is called a zwitterion. • A proton has been lost from the acidic carboxy group and the basic amino group has gained a proton. • The pH at which an amino acid exist as a zwitterion depends on the Z group

24. Zwitterions • Different forms of the zwitterion can exist depending on the acidity of the solution • Turn to page 190 for equations. • In acidic solutions the +H2N-CHZ-COOH form is most abundant. • In basic solutions the H2N-CHZ-COOH- form is most abundant. • The ability of amino acids to be both acids and bases means that they can act as buffers, minimising the effects of H+ or OH- ions. • This can be vital for some biochemical processes.

25. Protein Structure • A carboxy group can combine with an amine group via a condensation reaction. • This forms an amide functional group –CONH- • This can link two amino acids together to form a protein. • Remember a protein is a polymer made up of lots of amino acids.

26. Protein Structure • Molecules made from amino acids are often called peptides. • When two amino acid molecules react we get a dipeptide. • 3 form a tripeptide. • A polymer made from amino acids is called a polypeptide. • Polypeptides built from more than 50 amino acids are usually called proteins. • All polypeptides have the –CONH- linkage.

27. Proteins • Proteins differ from one another in the number, type and sequence of their constituent amino acids. • Each protein has a precise chemical composition, amino acid sequence and 3D shape. • The role that any protein fulfils in an organism depends on its shape. • This is regarded as being made up of a primary, secondary and tertiary structure.

29. Primary and secondary structures • Primary Structure • This is determined by the sequence of amino acids. • Secondary Structure • Involves hydrogen bonds between sections of the protein chain. • Can result in folding or coiling of sections of the protein.

30. Tertiary structure • Various types of attractions between NH and C=O influence the tertiary structure. • Other attractions such as ionic interactions, covalent cross-links between chains and dispersion forces can also determine the tertiary structure of proteins. • These forces mainly depend on the Z-chains of the amino acids. • Covalent cross linking occurs where two neighbouring cysteins react forming a –S-S- link.

31. Your Turn • Page 194 • Questions 13, 14 and 17

32. Enzymes: Biological catalysts • Catalysts control almost all the chemical reactions happening in our body. • The biological catalysts that accelerate the rate of chemical reactions in living things are a type of protein called enzymes. • Enzymes control the manufacture of complex substances, such as skin and blood, as well as the breaking down of chemicals to provide energy • Enzymes make life possible

33. Enzymes • Generally more efficient than inorganic catalysts. • They allow reactions to occur rapidly within the narrow band of temperatures in which life can survive. • A biological reaction often has a large number of stages • Each one controlled by its own enzyme

34. Enzymes vs inorganic catalysts • Compared to inorganic catalysts • Enzymes produce much faster reaction rates. • Enzymes operate under much milder conditions • Enzymes are more sensitive • Enzymes are very selective • Hundreds of enzymes have been isolated in pure form, ranging in size from molecules with relative molecular masses of 10,000 to molecules with relative molecular masses of several million

35. Enzymes • The catalytic activity depends on its tertiary structure. • A slight change in the its 3D shape can render an enzyme inoperable. • 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 ions, associated with the active site. • These cofactors may be necessary for the catalytic effect

36. How enzymes work • A reactant known as the substrate, is manoeuvred 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: • The substrate enters the active site • Bonds form between the enzyme and substrates weaken bonds within the substrate, lowering the reaction’s activation energy. • The substrate breaks or rearranges into new products and these products are released.

37. How enzymes work

38. Enzymes • In many cases, the enzyme and substrate bind together because part of the substrate and the active site are non-polar. • Dispersion forces are therefore significant • In other cases the substrate is held in place by an attraction between positive and negative charges: • attraction of a metal ion in the enzyme to a negative dipole on the substrate • Hydrogen bonding between enzyme and substrate

39. Enzymes • Here is shown the interactions at the active site of the enzyme responsible for catalysing a biochemical reaction in which a dipeptide consisting of leucine and histidine is chopped off the end of a short polypeptide chain.

40. Enzyme Selectivity • Enzymes are very selective and important in biological functions, each enzyme can only catalyse certain reactions. • The selectivity arises because of the shape and functional groups in the active site of the enzyme allow it to bind only with certain substrates. • The enzyme and substrate are often thought of as a lock and a key.

41. Denaturation • A change that destroys biological activity of a protein is called denaturation. • Denaturation may result because of: • Increased temperature • A pH change • Addition of various chemicals

42. Coagulation • Once a protein has been denatured, the unfolded chains tend to form randomly looped structure which come in close contact. • The chains become entangled and bond with each other • This causes large clumps of protein to form

43. Your Turn • Page 197 • Questions 19 - 21

44. Proteins as markers for disease • There are many proteins that indicate the presence of disease. • Some of the analytical techniques looked at earlier this year as well as 2D electrophoresis are used to identify these protein markers. • The body’s natural defences produce proteins called antibodies in the fight against infection caused by bacteria or viruses. • These antibodies are specific to a particular disease.

45. Protein markers • The cells in a diseased or damaged body organs may release specific proteins that are unique to that organ. • A raised level of these marker proteins in a patients blood or tissue can be used to: • Identify a disease at early or advanced stages of development • Monitor the progress of the disease • Measure the effectiveness of treatment • Test for the recurrence of the disease

46. Heart attack and prostate cancer • Read pages 198 – 199 • Your turn • Page 199 • Questions 22-23