Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings AP Biology Ch. 2 The Chemical Context of Life Bombardier Beetle’s Defense: Ejecting a spray of hot irritating chemicals, an example of the interconnectedness of biology and chemistry. Essential elements of life Structure of atoms Chemical bonding Chemical reactions

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 25 Essential Elements of Life 96% of living matter – O, C, H, N Table 2.1 Naturally Occurring Elements in the Human Body

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Effects of essential-element deficiencies (a) Nitrogen deficiency (b) Iodine deficiency – trace element Trace elements – required only in minute quantities deficiency results in great consequences 0.15 mg iodine required Malaysian woman – can be reversed with iodine supplements Figure 2.3

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings An element’s properties depend on the structure of its atoms. Atom – smallest unit of matter Mass number – sum of protons + neutrons Atomic number – Number of protons in the nucleus; 2 He Atomic weight – Mass number; 4 He Isotopes – 2 atoms of same element; differ in # of neutrons Nucleus Cloud of negative charge (2 electrons) Electrons Model of Helium

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Radioactive isotopes Unstable nuclei decay, emitting particles & energy Applications: date fossils trace atoms through metabolic processes diagnose disorders

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.5 Research Method Radioactive Tracers Scientists use radioactive isotopes to label certain chemical substances, creating tracers that can be used to follow a metabolic process or locate the substance within an organism. In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA. APPLICATION DNA (old and new) Ingredients including radioactive tracer (bright blue) Human cells Incubators °C 15°C20°C 25°C 30°C35°C 40°C 45°C 50°C TECHNIQUE 2 1 The cells are placed in test tubes, their DNA is isolated, and unused ingredients are removed Ingredients for making DNA are added to human cells. One ingredient is labeled with 3 H, a radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3 H. Radioactive isotopes – elements with unstable nuclei; give off particles and energy as they decay

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Placed in a Scintillation Chamber Temperature (°C) The frequency of flashes, - counts per minute, proportional to the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted against temperature, it is clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C Optimum temperature for DNA synthesis Counts per minute (x 1,000) RESULTS In scintillators the part of the energy lost by a particle is converted into the energy of a light flash

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 3 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar Chemical Behavior - determined by it’s electron configuration. Valence electrons – only unpaired electrons are involved Atoms with the same # of valence e- have similar chemical behaviors. nonreactive Figure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table.

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Formation & function of molecules depend on chemical bonding between atoms. Chemical bonds (4) – Covalent bond – – Ionic bond – – Hydrogen bonds – – van der Waals interactions –

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Covalent bonding – atoms sharing e- Name (molecular formula) Electron- shell diagram Structural formula (c) H Methane (CH 4 ). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane. Space- filling model Hydrogen (H 2 ). Two hydrogen atoms can form a single bond. (a) HH OO Oxygen (O 2 ). Two oxygen atoms share two pairs of electrons to form a double bond. (b) Water (H 2 O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water. OH H HH H O H OO H H H C H H H H C (d) Pair of equally shared e- Pair of unequally shared e- polar (e- shared unequally) vs. nonpolar (e- shared equally)

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Polar / Nonpolar Covalent Rules Nonpolar – e- shared equally -b/t 2 atoms of same element – H-H -b/t atoms w/similar electronegativity – CH 4 Polar – e- shared unequally ex. H 2 O; oxygen – higher electronegativity Electronegativity – attraction of an atom for the shared e- of a covalent bond (strong electronegative atoms attempt to pull the shared e- toward themselves)

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.12 Polar covalent bonds in a water molecule This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. H2OH2O –– O H H ++ ++ Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ionic bond – one atom strips e- from another cations (atom w/+ charge) anions (atom w/- charge) – The attraction between oppositely charged atoms, or ions, is an ionic bond. Cl – Chloride ion (an anion) – The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 1 Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. 2 Na Cl + Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na + Sodium ion (a cation) Sodium chloride (NaCl)

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydrogen bonds – – H atom of one compound is attracted to another compound – Holds water together Water (H 2 O) Ammonia (NH 3 ) –– ++ O H H ++ –– N H H H A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia. ++ ++ ++

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings van der Waals interactions – Molecules in close proximity exert attraction in concert Hair tip molecules and the molecules of the wall’s surface are so numerous, collectively they form strong bonding patterns temporarily. Gecko lizard – walks up walls

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecule’s biological function -related to its shape Biological molecules: – Recognize, interact with one another with a specificity based on molecular shape. Ex. morphine affects pain perception and emotional state by mimicking the brain’s natural endorphins. Natural endorphin Morphine Endorphin receptors

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chemical reactions make / break chemical bonds. Change reactants into products conserving matter Most are reversible. Chemical equilibrium is reached - when the forward and reverse reaction rates are equal Elodea, a freshwater plant, produces sugar by rearranging the atoms of carbon dioxide and water in the chemical process known as photosynthesis. Much of the sugar is then converted to other food molecules. Oxygen gas is a by-product of photosynthesis; hence the bubbles of oxygen escaping from the leaves.