CHAPTER 2: THE CHEMICAL CONTEXT OF LIFE AP Biology 1 CASE STUDY: DEVIL S GARDEN Ants use formic acid to maintain the garden of a single flowering tree called Duroia hirsuta Ants live in the hollow tree stems and prevent other species from growing by injecting the intruders with formic acid EXPERIMENT Duroia tree Devil s garden Cedrela sapling Insect barrier RESULTS Dead leaf tissue (cm 2 ) after one day 16 12 8 4 0 Cedrela saplings, inside and outside devil s gardens Figs. 2.1 & 2.2 2 MATTER Matter - anything that takes up space and has mass Made up of elements Sodium Chlorine Sodium chloride Fig. 2.3 Elements - substance that can not be broken down to other substances by chemical reactions Compound - substance containing two or more different elements combined together in a fixed ratio Compounds have characteristics different from those of their constituent elements 3
ESSENTIAL ELEMENTS 25 elements are essential for life Four make up 96% of living matter Trace elements - required by an organism in only minute quantitates 4 Atom - smallest unit of matter that still retains the property of that element ATOMS Cloud of negative charge (2 electrons) Nucleus Electrons Made up of subatomic particles: protons, neutrons, and electrons Atomic number - number of protons Mass number - roughly the sum of protons and neutrons (a) (b) Fig. 2.5 5 ISOTOPES Isotopes - atoms of a given element with more neutrons (thus a larger mass) Carbon isotopes - most common isotope of carbon is carbon-12 (99%), but some isotopes have extra neutrons (carbon-13 and carbon-14) Carbon-14 is not stable (radioactive) Radioactive isotope - an isotope in which the nucleus decays spontaneously, giving off particles of energy Radioactive isotopes are very useful in biology 6
RADIOACTIVE ISOTOPE USES Carbon dating Tracers TECHNIQUE TECHNIQUE 1 2 Human cells are incubated with compounds used to make DNA. One compound is labeled with 3 H. Cells from each incubator are placed in tubes; their DNA is isolated; and unused labeled compounds are removed. 35 C Compounds including Incubators radioactive tracer 45 C (bright blue) 10 C 15 C 20 C Human cells 10 C 15 C 20 C 10 15 20 25 30 35 40 45 50 DNA (old and new) 25 C 30 C 35 C 40 C 45 C 50 C Fig. 2.6 50 C 3 The test tubes are placed in a scintillation counter. RESULTS Counts per minute ( 1,000) 30 20 10 0 Optimum temperature for DNA synthesis 10 20 30 40 50 Temperature ( C) 7 RADIOACTIVE ISOTOPE USES PET scan allows radioactive isotopes to be used for medicine Cancerous throat tissue Fig. 2.7 8 Fig. 2.8 Figure 2.8 (a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons. ENERGY LEVELS Third shell (highest energy level in this model) Second shell (higher energy level) First shell (lowest energy level) (b) Atomic nucleus Energy absorbed Energy lost Energy - the capacity to cause change (to do work) Potential Energy - matter possesses it because of location and structure Energy levels describe the potential energy of an atom correlated with the average distance from the nucleus the average distances is represented symbolically as electron shells 9
ELECTRON SHELL DIAGRAMS First shell Second shell Hydrogen 1 H Lithium 3 Li Beryllium 4 Be Boron 5 B Mass number Carbon 6 C Nitrogen 7 N 2 He 4.00 Atomic number Element symbol Oxygen 8 O Electron distribution diagram Fluorine 9 F Helium 2 He Neon 10 Ne Third shell Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar Fig. 2.9 10 VALENCE ELECTRONS Valence electrons - outer electrons Valence shell - outermost shell Most chemical behaviors are dependent on the number of valence electrons 11 ELECTRON ORBITALS In reality we never know the exact path of an electron We then concentrate on where the electron spends the majority of its time Orbital - the three-dimensional space an electron spends 90% of its time Neon, with two filled Shells (10 electrons) (a) Electron distribution diagram First shell Second shell First shell Second shell z 1s orbital 2s orbital Three 2p orbitals (b) Separate electron orbitals x y no more than TWO electrons can occupy an orbital Fig. 2.10 1s, 2s, and 2p orbitals (c) Superimposed electron orbitals 12
CHEMICAL BONDING Covalent Bonds - sharing of a pair of valence level electrons by two atoms Molecule - two or more atoms held together by covalent bonds Types of covalent bonds: single bond - one shared pair of electrons Hydrogen atoms (2 H) double bonds - two shared pairs of electrons Structural formula vs. molecular formula Hydrogen molecule (H 2 ) Fig. 2.11 13 COVALENT BONDING (a) Name and Molecular Formula Hydrogen (H 2 ) Electron Distribution Diagram Lewis Dot Structure and Structural Formula Space- Filling Model (b) Oxygen (O 2 ) (c) Water (H 2 O) (d) Methane (CH 4 ) Fig. 2.12 14 ELECTRONEGATIVITY Electronegativity - attraction of a particular kind of atom for the electrons of a covalent bond The more electronegative an atom, the more strongly it pulls its shared electrons toward itself Non-polar covalent bond - electrons are shared equally (usually because the elements are the same) Polar covalent bond - electrons are not shared equally δ O H H H 2 O Fig. 2.13 15
IONIC BONDS Electrons are so unequal in attraction to valence electrons that the more electrons the more electronegative atom strips the electron from its partner Ex. NaCl + Ion - charged atom Na Sodium atom Cl Chlorine atom Na + Sodium ion (a cation) Cl Chloride ion (an anion) Sodium chloride (NaCl) Cation - positively charged ion Anion - negatively charged ion Na + Cl Figs. 2.14 & 2.15 Attraction between cation and anion causes ionic bonds Compounds formed by ionic bonding are called ionic compounds or salts 16 HYDROGEN BONDS Extremely important form of bonding in biological systems Water (H 2 O) δ Forms when a hydrogen atom is covalently bonded to one electronegative atom is also attracted to another electronegative atom δ Hydrogen bond These electronegative atoms are usually oxygen or nitrogen Fig. 2.16 17 VAN DER WAALS INTERACTIONS Even molecules with nonpolar covalent bonds have positive and negative regions Because electrons are in constant motion, at any instant they may accumulate by chance in one part of the molecule Van der Waals Interactions are very weak and occur only when molecules are very close together Give geckos the ability to climb up a surface 18
MOLECULAR SHAPE Shape is directly related to function s orbital z x Four hybrid orbitals Three p orbitals Determined by the position of electrons in the valence shell Orbital hybridization In covalent bonding, s and p orbitals hybridize creating specific shapes (a) Hybridization of orbitals Space-Filling Model Water (H 2 O) y Ball-and-Stick Model Tetrahedron Hybrid-Orbital Model (with ball-and-stick model superimposed) Unbonded Electron pair Tetrahedral shape (bond angles = 109 degrees) Methane (CH 4 ) (b) Molecular-shape models Fig. 2.17 19 MOLECULAR SHAPE Molecular shape also determines how biological molecules recognize and respond to one another Natural endorphin Carbon Hydrogen Morphine Nitrogen Sulfur Oxygen Only molecules with complementary shape are able to bind to each other (usually with hydrogen bonds) Ex. endorphins (a) Structures of endorphin and morphine Natural endorphin Brain cell Endorphin receptors (b) Binding to endorphin receptors Morphine Fig. 2.18 20 CHEMICAL REACTIONS Making and breaking of chemical bonds leading to changes in the composition of matter Eventually the the relative concentrations of reactants and products stop changing. This is called chemical equilibrium. 2 H 2 + O 2 2 H 2 O Reactants Reaction Products 21