CHAPTER 2 The Nature of Molecules

Which Elements Are Most Significant To Biologists? Six of these plus a few other trace elements

Figure 2.3 Nitrogen deficiency All plants need nitrogen to grow. Do you know why?

Heavy isotopes are used As biological Tracers Do you know Why? ISOTOPES 3 H hydrogen (tritium) 14 C carbon 32 P phosphorous 35 S sulfur 131 Iiodine

Figure 2.8 The Tokaimura nuclear accident

RADIOACTIVE TRACERS Examples of how biologists use isotopes to trace specific molecules AUTORADIOGRAPHY - locate specific molecules within cells w/ X-ray film SCINTILLATION COUNTER - follow and chart metabolic activity within cells PET SCAN - Positron Emission Tomography reveals location of intense chemical activity

Figure 2.6 Using radioactive isotopes to study cell chemistry

Figure 2.4 Goiter Iodine is used to trace thyroid problems

Figure 2.5 Two simplified models of a helium (He) atom

Figure 2.9 Energy levels of an atom’s electrons

Figure 2.11 Electron orbitals

Figure 2.10 Electron configurations of the first 18 elements

IONIC BONDS the transfer of electrons loss of electron(s) cation gain of electron(s) anion dissociate in aq. soln.

Figure 2.15 A sodium chloride crystal

COVALENT BONDS sharing of electron pairs strong bonds in aqueous solution The most common bond in organic molecules

COVALENT BONDS sharing of electron pairs strong bonds in aqueous solution NONPOLAR COVALENT BOND CH 4 C & H equal affinity for electrons

Figure 2.12x Methane What is the shape of this molecule? Why does this molecule have this shape?

COVALENT BONDS POLAR COVALENT BOND H2OH2O ELECTRONEGATIVITY each atom in polar bond has partial charge creating opposite poles or polarity remember O and N bonded to H

Figure 2.13 Polar covalent bonds in a water molecule

HYDROGEN BONDS weak bonds bonds between polar molecules or polar parts of large macromolecules. H-bonds give macromolecules their 3-D shape. hydration shells water forms hydration shells around ions

HYDROGEN BONDS You must understand hydrogen interactions to understand biochemistry

Hydrophobic Interactions nonpolar w/ nonpolar squeeze out water Important in shaping and organizing the molecules of life

Most Common Bond in Life Covalent Bond Electrons are shared Overlapping orbitals & lack of charge strong in aqueous solution

Covalent bonds are not all created equal Nonpolar Covalent atoms share electrons equally Example: O 2 CH 4 Polar Covalent Atoms shared electrons unequally Slightly positive and slightly negative pole H 2 O NH 3 Hate hanging out w/ water Love hanging out w/ water Why?????

Hydrogen Bonds

Hydrogen Bond Technically these are Fake Bonds Interactions between polar molecules molecules with slightly charged poles can hydrogen bond sticky

Hydrogen bonds give water many special properties sticky Effects on Temperature Great solvent Also very important Determines 3D shape of many organic molecules!!!!!

The Medium of Life hydrophobic Vs. hydrophilic Biochemistry is wet chemistry Only molecule found in all three states on the surface of the earth

Hydrogen bonds give water many special properties sticky

Hydrogen bonds help determine the shape of macromolecules

Review of some helpful terms Atoms Molecules Macromolecules ProtonsFunctional GroupsCarb’s NeutronsNonpolarLipids ElectronsPolarProteins Nucleic Acids IonsInorganic IsotopesOrganic How are these used? How do these How do these differ? differ?

An the most important Love/Hate Relationship on earth Hydrophobic Hydrophilic

3-D shape is essential to structure/function

Unnumbered Figure (Page 38) Chemical reaction between hydrogen and oxygen

Figure 2.20 Photosynthesis: a solar-powered rearrangement of matter The bubbles are evidence that ???? Is taking place Can you fill in the ?????