1 Life and Chemistry: Small Molecules

2 Life and Chemistry: Small MoleculesWater and the Origin of Life’s Chemistry Atoms: The Constituents of Matter Chemical Bonds: Linking Atoms Together Water: Structure and Properties Acids, Bases, and the pH Scale Properties of Molecules Chemical evolution Amino Acids

3 Please recall or learn from bookAtom, Atom structure, Proton, Neutron, Electron Elements, Periodic table, Isotopes, Orbitals Molecules,Chemical bonds & interactions Isomers, Optical isomers Chemical reactions, Reactants, Products, Bond energy Mole, Molar pH, Buffers Chapter 2 in “Life” or in “Biology” or in “Cell Biology”

4 Chemical Bonds: Linking Atoms TogetherA covalent bond is formed by sharing of a pair of electrons between two atoms. In hydrogen molecules (H2), a pair of electrons share a common orbital and spend equal amounts of time around each of the two nuclei. The nuclei stay some distance from each other due to mutually repelling positive charges.

5 Chemical Bonds: Linking Atoms TogetherCovalent bonds are very strong. Each covalent bond has a characteristic length, angle, and direction, which makes it possible to predict the three-dimensional structures of molecules.

6 Chemical Bonds: Polar covalent bondsElectrons are not always shared equally between covalently bonded atoms. The attractive force that an atom exerts on electrons is called electronegativity. When a molecule has nuclei with different electronegativities, an electron spends most of its time around the nucleus with the greater electronegativity. resulting in a polar covalent bond. Water: A polar molecule Electronegativity O = 3.5 H = 2.1

7 Chemical Bonds: Hydrogen bondsHydrogen bonds may form within or between molecules with polar covalent bonds. Atoms bound by Hydrogen bonds do not share electrons. Although hydrogen bonds are weak, they tend to be additive (10 hydrogen bond equal 1 covalent bond), and they are of profound biological importance.

8 Chemical Bonds: Ionic bondsIons are formed when an atom loses or gains electrons (becomes charged). Ionic bonds are formed by the electrical attraction between ions with opposite charges. Electronegativity

9 Polar molecules in waterWhen salt is introduced into water, the partial charges of the water molecules can easily interfere with the ionic bonds.

10 Chemical Bonds: Hydrophilic moleculesSubstances that are ionic or polar often dissolve in water due to hydrogen bonds, and are called hydrophilic.

11 Chemical Bonds: Hydrophobic interactionsNonpolar molecules are called hydrophobic because they tend to avoid water and aggregate with other nonpolar molecules. (Oil) C H 2.5 electronegativity

12 Chemical Bonds: Hydrophobic & Van der Waals forcesNonpolar molecules are also attracted to each other via relatively weak attractions called van der Waals forces, which are brief interactions induced by random variations in electron distribution A single van der Waals interaction is weak but large non-polar molecules' can form many interactions

13 Chemical Bonds: Van der Waals forcesA single van der Waals interaction is weak but large non-polar molecules can form many interactions Gecko foot Artificial Gecko tape Made of Carbon nanotubes Can hold four times what geckos can Can stick to Teflon Stickybot_ mov

14 Non-Covalent bonds Non-covalent

15 The Molecule That Supports All of LifeWater is the biological medium on Earth All living organisms require water more than any other substance Most cells are surrounded by water, and cells themselves are about 70–95% water The abundance of water is the main reason the Earth is habitable The water molecule is a polar molecule: The opposite ends have opposite charges Polarity allows water molecules to form hydrogen bonds with each other. Each molecule forms hydrogen bonds with four other molecules.

16 Water: Structure and PropertiesDue to its shape, polarity, and ability to form hydrogen bonds, water has some unusual properties. Water expand upon freezing: Ice is held in a crystalline structure by the orientation of water molecules’ hydrogen bonds. Ice is structured but not packed = Ice floats allowing life under the ice. Energy allows bond to break

17 Water: Structure and PropertiesA calorie (cal) is the amount of energy (heat) required to raise the temperature of 1 g of water by 1°C The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC The specific heat of water is 1 cal/g/ºC Liquid water has a higher specific heat than most other small molecules in liquid form (ethanol 0.6 cal/g/ºC). The high specific heat of water minimizes temperature fluctuations to within limits that permit life

18 Water: Structure and PropertiesThe heat of vaporization is the amount of heat needed to change a substance from liquid state to gaseous state. A lot of heat is required to change water to a gaseous state because the hydrogen bonds of the liquid water must be broken. Evaporation has a cooling effect by absorbing calories.

19 Water: Cohesion & adhesionWater has a cohesive strength because of hydrogen bonds. The cohesive strength of water molecules allows the transport of water from the roots to the tops of trees.

20 Water: Structure and PropertiesWater has high surface tension, which means that the surface of liquid water is relatively difficult to puncture.

21 Acids, Bases, and the pH ScaleWater has a slight tendency to ionize into a hydrogen ion and a hydroxide ion H2O ↔ H+ + OH– The H+ ion is formed as Hydronium ion. The concentration of hydrogen ions is 1 x 10–7 moles per liter of water. This ionization is very important for living creatures and the chemical reactions they must perform because the H+ ion is so reactive. One in 500,000,000

22 The pH Scale pH is the measure of hydrogen ion concentration It is defined as the negative logarithm of the hydrogen ion concentration in moles per liter. = -log10[H+]. A pH 7 means the concentration of hydrogen ions is 1 x 10–7 moles per liter of water. The pH scale indicates the strength of a solution of an acid or base. The scale values range from 1 through 14.

23 Acids, Bases, and the pH ScaleSubstances that dissolve in water and release hydrogen ions (H+); are called acids. Substances that dissolve in water and capture hydrogen ions are called bases. Most bases are substances that release hydroxide ions (OH–) when dissolved in water. Hydroxide ions can bind with a hydrogen ion to form water: H2O ↔ H+ + OH– Acids donate H+; bases accept H+.

24 Acids Acids release H+ ions in solution. If the reaction is complete, it is a strong acid, such as HCl. HCl ® H+ + Cl- The carboxyl group (—COOH) is common in biological compounds. It functions as an acid because —COOH ↔ —COO- + H+

25 Bases Bases accept H+ in solution. NaOH ionizes completely to Na+ and OH–. The OH– absorbs H+ to form water. It is a strong base. The amino group (—NH2) is an important part of many biological compounds; it functions as a weak base by accepting H+: —NH2 + H+ ↔ —(NH3)+

26 Acids, Bases, and the pH ScaleIonization of strong acids is virtually irreversible. HCl ® H+ + Cl- Ionization of weak acids and bases is somewhat reversible. Many large molecules in biological systems contain weak acid or base groups.

27 Properties of MoleculesFigure pH Values of Some Familiar Substances Properties of Molecules

28 Figure 2.19 Buffers Minimize Changes in pHpH of blood is 7.4 and is normally very stable (pH of 7 or 7,8 means death). Organisms are able to maintain stable pH In the blood, this is achieved by the presence of Bicarbonate and Carbonic acid. Together they form a buffer system Addition of reactants to one side of a reaction drives the reaction in the direction that uses that component. H+ + HCO3-  H2CO3 Bicarbonate Carbonic acid

29 Figure 2.19 Buffers Minimize Changes in pHCO2+H2O  H+ + HCO3-  H2CO3 Bicarbonate Carbonic acid

30 Acids, Bases, and the pH ScaleOrganisms regulate (buffer) pH and depend on it. A buffer is a mixture of a weak acid and its corresponding base. Because buffers can react with both added bases and acids, they make the overall solution resistant to pH change. H+ + HCO3-  H2CO3 Bicarbonate Carbonic acid

31 Elements of life

32 Required in trace amountsElements of life Life prefers low molecular whight Lime stone = evidence of life =99% Required in trace amounts =0.9% Found (not clear if required)

34 Organic Molecules 99% of live material is made of molecules composed of: C,H,O,N The basis of most organic molecules is a carbon skeleton The properties of each molecule are determined by its composition and spatial organization.

35 Functional groups in organic chemistryDistinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it A number of characteristic groups are often attached to skeletons of organic molecules. These are called functional groups Functional groups are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties Estradiol Testosterone

36 Functional groups in organic chemistryImportant functional groups include: Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group

37 Hydroxyl group Ethanol, the alcohol present inEXAMPLE STRUCTURE Ethanol, the alcohol present in alcoholic beverages In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) FUNCTIONAL PROPERTIES Is polar as a result of the electrons spending more time near the electronegative oxygen atom. NAME OF COMPOUND Alcohols (their specific names usually end in -ol) Sugars Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

38 Carbonyl group The carbonyl group ( CO) consists of a carbon atomSTRUCTURE EXAMPLE Acetone, the simplest ketone The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. Propanal, an aldehyde Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. NAME OF COMPOUND Aldehydes if the carbonyl group is at the end of the carbon skeleton These two groups are also found in sugars, giving rise to two major groups of sugars: aldoses (containing an aldehyde) and ketoses (containing a ketone).

39 Carboxyl group

40 Amino group

41 Methyl group

42 Phosphate group

43 Sulfhydryl group

44 Water and the Origin of Life’s ChemistryThe earliest chemical signatures of life on Earth are about 4 billion years old. The presence of water, possibly brought by comets striking the Earth, was critical in making conditions suitable for life. Environmental conditions conducive to life evolved during the Hadean period.

45 Figure 2.1 A Geological Time Scale

46 Theories of the Origin of LifeLiving things are composed of the same elements as the universe. The arrangement of these elements in biological systems is unique. There are two theories for the origin of life during the 600 million years of the Hadean: Life from extraterrestrial sources Chemical evolution

47 Theories of the Origin of LifeCould life have come from outside Earth? The composition of meteorites suggests that some of life’s complex molecules could have come from space. There is no proof, however, that living things have ever traveled to Earth by way of a comet or meteorite.

48 Theories of the Origin of LifeThe theory of chemical evolution holds that conditions on the primitive Earth led to the formation of the large molecules unique to life. In the 1950s, Stanley Miller and Harold Urey set up an experimental “primitive” atmosphere and used a spark to simulate lightning.

49 Methane Ammonia Hydrogen Water Nitrogen Amino acids Nucleic acidsFigure 3.1 Synthesis of Prebiotic Molecules in an Experimental Atmosphere Methane Ammonia Hydrogen Water Nitrogen Amino acids Nucleic acids Hydrogen Water Nitrogen

50 Theories of the Origin of LifeThe results of the Miller-Urey experiments have undergone several interpretative refinements (Volcanic eruptions contribute sulfur). The earliest stages of chemical evolution resulted in the emergence of monomers and polymers that probably have remained generally unchanged for 3.8 billion years.

51 Amino acids General structure of amino acids a Amine Carboxyl

52 Amino acids Amino acids in water a H3N+ H+ +  -COO- + H+

53 Amino acids Condensation reaction releases water and creates a peptide bond

54 Table 3.2 The Twenty Amino Acids Found in Proteins (Part 1)

55 Table 3.2 The Twenty Amino Acids Found in Proteins (Part 2)

56 Table 3.2 The Twenty Amino Acids Found in Proteins (Part 3)