The Chemical Context of Life

Elements of LifeAtoms, Molecules & Compounds

Chemical BondsStructure and Function

Chemical Reactions

Organic Chemistry

Chemistry is fundamental to understanding lifeReactions at the molecular level based in rules of bonding and reactions “run” the machinery of lifeChemicals are required for growth, defense, development and many other reactions in living organisms

Figure 2.1 The hierarchy of biological order from atom to organism

Figure 2.0 Bombardier beetle

Organic Chemistry (Continued)

You must understand the elements within living things and understand how they combine to form the four basic organic compoundsA knowledge of how atoms bond and atomic structure is crucialLet’s look at the main elements found in living things

Table 2.1 Naturally Occurring Elements in the Human Body

Atomic Bonding

Remember that atoms bond based on the number of unpaired electrons in their valence or outer shell.Each filled shell has a specific number of electrons (1st shell 2, Second shell 8)There can be two electrons in each orbital. Each orbital fills one electron at a time.Carbon has four unpaired electrons, within four orbitals.This gives it four bonding sites and makes it a versatile compound for living things

Valence NumbersThe valence number is the number of unpaired electrons in the outer shellYou should know at least the first ten most common elements in living things and their valence numbersNormally, unpaired electrons will bond with electrons of other elements to fill the outer shellIt is how atoms bond (angles, electronegativity, types of bonds) that determine a compound’s characteristics

Figure 2.10 Electron configurations of the first 18 elements

Energy Levels of ElectronsThe more distant an electron is from the nucleus the more potential energy it storesEnergy levels are the different states of potential energy that electrons have in an atomElectrons may absorb energy and move to a higher level or fall to a lower level and release energyThis is important in one complex reaction we will study-photosynthesis

Figure 2.9 Energy levels of an atom’s electrons

CompoundsRemember also that a compound will usually have emergent or different properties than the individual properties of the elements that make it up.

Figure 2.2 The emergent properties of a compound

Sodium + Chlorine = Table Salt

Emergent Properties in a compound

Types of Bonds in Living Things

There a number of strong and weak bonds in living thingsYou should be familiar with ionic and covalent bonds already, but we will review them.There are also weak bonds important to some molecules and solutions in living things.

Covalent BondsCovalent bonds are strong bonds that occur when electrons are shared.Examples of covalent bonds are on the following slidesA type of bond called a polar covalent bond occurs when an atom that has a high electronegativity pulls atoms of other elements closer to itself than is normal (Example: water)

Figure 2.12 Covalent bonding in four molecules

Figure 2.13 Polar covalent bonds in a water molecule

Ionic BondsIonic bonds occur when electrons are stripped from one atom and transferred to another (Sodium and Chlorine is an example when salt forms)This causes each atom to become either a cation (atom with a + charge) or an anion (atom with a – charge)Ionic compounds those formed by ionic bonds

Figure 2.14 Electron transfer and ionic bonding

Important Weak Bonds Van der Waals interactions form weak bonds and only occur when the atoms are very close to one anotherThey are due to the fact that electrons are in motion all the time and cause some charge to occur in even nonpolar covalent bonds.

Hydrogen BondsHydrogen bonds form between molecules of polar covalent compounds when there is a very slight difference in charge between two of them.They are a relatively weak bonds, but give water some of its more unique properties.

Figure 2.16 A hydrogen bond

Atoms, bonds and ShapeWhen atoms bond to one another, the positions of their orbitals determine the molecular shapeSometimes orbitals can mix or hybridize in specific ways to give a molecule a specific shape

Figure 2.17 Molecular shapes due to hybrid orbitals

The Shapes of Biological Molecules

The shapes of biological molecules determine their functionEnzymes and neurotransmitters are examples of molecules whose shapes are crucial to their functionsReceptors on the neuronal cell membrane “fit” specific neurotransmitters which then cause the neighboring neurons to fire

Figure 2.18 Molecular shape and brain chemistry

Molecular MimicsIf a particular molecule, say from a drug, is similar to that of a molecule in the body, it can occupy receptors for that molecule in the body and affect itExample: Endorphins are our brain’s pain and pleasure chemicalsDrugs like morphine and heroin can occupy the same receptors as these, causing powerful reactions in the brain

Figure 2.19 A molecular mimic

Chemical ReactionsChemical reactions make or break the bonds between atoms and moleculesIf bonds are broken, energy is releasedEnergy is used to make bondsReactants are what go inProducts are what come outChemical equilibrium is the point where relative concentrations of reactants and products stop changing

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