1. 1 GEK1530 Frederick H. Willeboordse frederik@chaos.nus.edu.sg Nature’s Monte Carlo Bakery: The Story of Life as a Complex System

2. 2 Atoms, Bonds, Carbohydrates & Fats Lecture 1 This lecture starts with the most basic building blocks, atoms, and shows how they combine in organic and inorganic matter.

3. GEK1530 3 The Bakery Add Ingredients Process Flour Water Yeast Knead Wait Bake Get some units - ergo building blocks Eat & Live Get something wonderful! mix n bake

4. GEK1530 4 The Simplest Unit - Water Oxygen Hydrogen How do these combine? To answer that we first need to ask Where do they come from? What do they consist of?

5. GEK1530 5 How it all started Let’s start at the beginning… Hubble picture of NGC6822 (NASA) About 13 billion years ago there was a ‘big bang’ that created our universe. At first our universe was very hot consisting of what one could call ‘melted’ matter. After a few hundred thousand years it had cooled to the point where matter ‘condensed’ to the form that still exists today.

6. GEK1530 6 Matter Most of the matter was Hydrogen and Helium and a few other light elements. This compacted into stars where the lighter elements were burnt yielding heavier elements (up to iron). Even heavier elements (like lead and gold) were created in supernovae. All in all a bit more than 100 elements are known but only a few of them are important for life. Hubble picture of IC4406 (NASA)

7. GEK1530 7 Star Systems Some of the ‘leftovers’ from supernovae (combined with varying amounts of the original matter) lead to solar systems with planets. Earth is one such planet and life originated around 4 billion years ago probably as a simple bio-chemical process. Supernova 1987A

8. GEK1530 8 The smallest unit of an element is the atom. Atoms are built up from only 3 types of so-called elementary particles. Protons, neutrons and electrons. Atoms The simplest atom is the Hydrogen atom. It consists of one proton and one electron. Protons have an electric charge of +1, neutrons have no electric charge and electrons have an electric charge of -1.

9. GEK1530 9 Core of Galaxy NGC4261 (NASA) A massive black hole! In their basic state, atoms are neutral and that means that they have as many electrons as protons. The electrons are arranged in so- called shells around the nucleus (the central part of the atom where the protons and neutrons reside). The chemical properties of the atoms are mainly determined by the number of electrons in the outermost shell. Atoms

10. GEK1530 10 This figure shows, schematically, how the electrons are arranged in shells H Li He Be B C N O F Ne Now there’s a key property: Atoms like it when shells are full. H - Hydrogen Li - Lithium Be - Beryllium B - Boron C - Carbon N - Nitrogen O - Oxygen F - Carbon He - Helium Ne - Neon Atoms

11. GEK1530 11 That means: H Li He Be B C N O F Ne He and Ne are very happy (hence they hardly react and are therefore called noble gasses). Li has an electron too ‘many’ and F an electron too ‘little’. In the same way, O has 2 electrons too ‘little’ H is a bit special …. The physical/chemical basis of all life is the fact that atoms can interact and form “bonds”. Atomic Bonds

12. GEK1530 12 Covalent Bond Each hydrogen atom has only 1 electron. This is one too little for a complete first shell. Take 2 hydrogen atoms One possibility would be that one atom gives up an electron and the other receive one electron. Then the two hydrogen ions could form a so- called ionic bond. (In fact this is not a stable configuration and hence does not occur). H H HH H+H+ H-H-

13. GEK1530 13 Ionic bonds are not so strong, however, and it turns out that there is an energetically more favorable solution: Sharing! HH Like this each atom has in a sense two electrons. This is called a covalent bond and it is quite strong. Covalent Bond Atoms can share a single electron but (depending on the element) also two or three electrons. E.g. in carbon double bonds are quite common. C C H H H H Ethylene

14. GEK1530 14 Water Now let’s get back to water Here we have to combine one oxygen with two hydrogen atoms. H H O One electron too little for a full shell. Two electrons too little for a full shell

15. GEK1530 15 Water (H 2 O) is formed by covalent bonding of two Hydrogen atoms and one Oxygen atom. H H At first one might think it looks somewhat like this. O However, this is not really the case. The six electrons of the Oxygen (repelling each other due to their equal charges) want to be as far from each other as possible. Covalent Bond

16. GEK1530 16 H H In a covalent bond, the pairing electrons of two atoms want to overlap as much as possible while staying away from other electrons as far as possible. Hence in first instance we’ll get a 90 o arrangement. O This can be achieved by basically in this way: The electrons spread out along the x,y,z axis x,y,z-axes Covalent Bond

17. GEK1530 17 Since equal charges repel, the two hydrogen atoms will be pushed out a bit. This then leads to water’s ‘V’ shape. The Oxygen atom turns out to pull at the electrons a bit harder than the Hydrogen atom. Consequently, there is a slight charge shift towards the Oxygen atom. H H O bit - bit + bit + bit - H H O bit + bit - bit + Of course, one would really need quantum mechanics to explain what’s going in detail. Covalent Bond

18. GEK1530 18 Chime - Water H H O bit - bit + bit - bit + Van der Waals Radii Ball and Stick

19. GEK1530 19 So we’ve seen that atoms stick together due to bonds. Are there other bonds? Yes: Polar Bond Ionic Bond Vd. Waals Bond Metallic Bond Let’s have a look a some of these Atomic Bonds

20. GEK1530 20 Polar Bond A covalent bond that leads to one side of a molecule having a bit a different net charge than the other is called a polar covalent bond and this in turn gives rise to another type of electrostatic bond. H H O bit - bit + bit - bit + H H O bit - bit + bit - bit + Attractive force. When one of the atoms involved is hydrogen, this bond is called a hydrogen bond and of particular importance in biology. The hydrogen bond

21. GEK1530 21 Ionic Bonds NaCl Sodium has one electron too many. Chlorine has one electron too little. Na + Cl - Sodium thus becomes a positively charged ion. Chlorine thus becomes a negatively charged ion. When Na and Cl come close, Na can give up an electron to Cl. We then have two ions with opposite charges that attract each other. This attractive force can hold the ions together to form a compound we all know. SALT. This bond is called ionic bond.

22. GEK1530 22 vd Waals Interaction Van der Waals Interaction Lastly, when molecules or parts of larger molecules are nearby, the electrons can behave in a synchronized way such that they avoid each other as much as possible. The net result of this interaction is a very weak attractive force. This is called:

23. GEK1530 23 J. D. van der Waals Nobel Prize in Physics 1910 Born: 23 Nov 1837 in Leyden, Holland Died: 8 Mar 1923 in Amsterdam, Holland First was a school teacher because he didn’t know the classical languages which were required for obtaining university degrees when he was young. After the laws changed, he obtained his doctorate degree at age 36 with a ground-breaking study on the transition from gaseous to liquid form. He was the first one to realize that the volumes and intra-molecular forces of atoms and molecules were necessary to establish the relationship between pressure, volume and temperature of liquids and gasses. Johannes Diderik van der Waals

24. GEK1530 24 Relative Strengths Covalent Bond: Ionic Bond: Polar Bond: Vd Waals: ~ 35-110kilocalories/mole ~ 10 kilocalories/mole ~ 4-5 kilocalories/mole ~ 1-2 kilocalories/mole In aqueous solutions calorie (with a small c): The energy required to raise the temperature of 1g of water from 14.5 to 15.5 degrees centigrade. Mole: That amount of any particular substance having a mass in grams numerically the same as its molecular or atomic weight. Note: 1c ~ 4.186J; The energy content of fat ~ 9kcal/g, proteins & carbohydrates ~ 4kcal/g

25. GEK1530 25 Water Back to water again Although not really a complex system we already see that the properties of water are very different from its building blocks Hydrogen and Oxygen. E.g. Liquid more dense than solid Solubility: Polar like water will dissolve ionic compounds and covalent compounds which ionize.

26. GEK1530 26 Flour Typical White Wheat Flour Composition: Carbohydrates66 Water11 Fiber10 Protein9 Fat2 Ash2 The most common is carbohydrate which is, as the name indicates, based on carbon. So let’s have a closer look at carbon.

27. GEK1530 27 Carbon Why is carbon so important? Four unpaired electrons available for covalent bonding Many possibilities to molecules Carbon is quite abundant GraphiteCoal Diamond

28. GEK1530 28 Hydrocarbons Carbon easily bonds with other carbons and with hydrogen Substitution of other atoms leads to derivative hydrocarbons. There are more than half a million of these in nature. H H C H H C H H C H H H C H H H C H H C H H C H H H H H C H H C H C H H C H H H C H H C H H C H Cyclopropane Isobutane Butane Propane Chained C Branched C Cyclic C

29. GEK1530 29 Chime - Hydrocarbons

30. GEK1530 30 Functional Groups Many hydrocarbons and other organic compounds have so-called functional groups attached to them. These are often used in the names of these compounds. Some of the major functional groups are: Amino Phosphate N H H P O OH Carboxyl C O OH Aldehyde C O H

31. GEK1530 31 Carbohydrates Aldehyde C O H With the aldehyde group, simple carbohydrates like glucose can be made. Pure carbohydrates contain carbon, hydrogen and oxygen in a 1:2:1 ratio but there are also deviations like in e.g. the famous deoxyribose. Haworth projection Glucose A Haworth projection has the following characteristics: Carbon is the implicit type of atom. In the example on the right, the atoms numbered from 1 to 6 are all carbon atoms. Hydrogen atoms on carbon are implicit. In the example, atoms 1 to 6 have extra hydrogen atoms not depicted. A thicker line indicates atoms that are closer to the observer. In the example on the right, atoms 2 and 3 (and their corresponding OH groups) are the closest to the observer, atoms 1 and 4 are further from the observer and finally the remaining atoms (5, etc.) are the furthest.

32. GEK1530 32 Glucose, also a product of photosynthesis, is used as a source of energy in plants and animals. Glucose can be a building block. It can combine with other glucose molecules to from long structures. In chemistry, a simple molecular structure that can somehow chain together to from big structures is called a monomer while the resulting big structure is called a polymer. The carbohydrate we find in flour consists of such glucose polymers (this gives starch) Carbohydrates

33. GEK1530 33 Chains with C We have seen how combining carbon leads to sugars and starch. Do we have something else? Lipids Fat or fat-like compounds. In their simplest form they are hydrocarbons with a carboxyl group at one end. Fats consist of glycerol and fatty acids Carboxyl C O OH

34. GEK1530 34 Larger molecules H C H H H C H H C H H C H H C H H C H H C H H C H H C H OH C O H C H H C H H C H H C H H C H H C H H C H Palmitic Acid – one type of fatty acid (e.g. lard is about 25% made of palmitic acid). Larger Molecules are obtained by stringing together many of these elements. This kind of element is non-polar and thus not soluble in water. The simplest lipid is a fatty acid. It consists of a hydrocarbon chain with a carboxylic acid at one end.

35. GEK1530 35 Acids An acid is a substance that increases the concentration of Hydrogen (H + ) ions in water A base is a substance that decreases the concentration of Hydrogen (H + ) ions in water Ammonia Hydrochloric Acid

36. GEK1530 36 H H H C H H C H H C H H C H H C H H C H H C H H C H O C O H C H H C H H C H H C H H C H H C H H C H H C H H C H H H C H H C H H C H H C H H C H H C H H C H H C H O C O H C H H C H H C H H C H H C H H C H H C H H C H H C H H H C H H C H H C H H C H H C H H C H H C H H C H O C O H C H H C H H C H H C H H C H H C H H C H H C H H C H C C C H H H H Glycerol Fatty acid Hydrocarbon chain Tristearin Tristearin is a common animal fat

37. GEK1530 37 Fats Fats and building blocks Again, although just as water not really a complex system we see that the properties of fat are very different from its building blocks Carbon, Hydrogen and Oxygen. Would a ‘small’ change to the structure matter?

38. GEK1530 38 Soap H H C H H C H H C H H C H H C H H C H H C H H C H O-K+O-K+ C O H C H H C H H C H H C H H C H H C H H C H A potassium soap. Mixing this with table salt solution (NaCl) one can replace the Potassium ion with an Sodium ion to obtain the softer Sodium soap. If one takes a fat like tristearin on the previous slide and heats it with an alkaline substance like potassium hydroxide (KOH), one obtains soap. Polar

39. GEK1530 39 H H C H H C H H C H H C H H C H H C H H C H H C H O-K+O-K+ C O H C H H C H H C H H C H H C H H C H H C H The tail, however, is hydrophobic and hence soluble in oil. The head is hydrophilic and hence soluble in water. Soap

40. GEK1530 40 In this way the grease can be rinsed away. As a result of the head-tail properties, soap molecules in water can from micelles with grease on the inside. Water Schematic representation of a soap molecule Soap

41. GEK1530 41 Key Points of the Day Building Blocks Bonds Sugars Fat/Soap

42. GEK1530 42 Give it some thought! What is a bakery?

43. GEK1530 43 References