The Chemistry of Life Biology is a multidisciplinary science. Living organisms are subject to basic laws of physics and chemistry. One example is the bombardier beetle, which uses chemistry to defend itself.

Atoms of elements play important roles in biology What element is lacking in her diet?

Atoms combine to make molecules The bonds between atoms of the same molecule are intramolecular bonds. The three types of intramolecular bonds are: 1.Covalent Bonds 2.Ionic Bonds 3.Polar Covalent Bonds

1. Covalent Bonds The bond is formed by sharing a pair of valence electrons between two atoms. The bond can be represented in many ways. Hydrogen (H 2 ) Name (molecular formula) Electron- shell diagram Structural formula Space- filling model

2. Polar Covalent Bonds This bond occurs when a pair of valence electrons is unequally shared between two atoms. The atom with a larger nucleus attracts the electron more and has a slightly negative charge. The other atom is slightly positive.

3. Ionic Bond Formed by the transfer of an electron from atom to atom. This results in the formation of positive cations, and negative anions. Ions are held together by electrostatic attraction. Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na + Sodium ion (a cation) Cl – Chlorine ion (an anion) Sodium chloride (NaCl)

Properties of Covalent Bonds Pure Covalent Bonds Results from largely equal sharing of electrons. Happens when bond partners have similar electronegativities or an electronegativity difference of <0.5 Polar Covalent Bonds Results from unequal sharing of electrons. Happens when bond partners have electronegativity differences between 0.5 and 1.6

The Role of Electronegativity Electronegativity is a measure of the strength with which an atom can attract electrons and can be found on a periodic table. The electronegativity difference between two atoms is calculated by subtracting the smaller value from the larger value.

Bond Types and Electronegativity A difference of < 0. 5  covalent bond A difference of 0.5 – 1.6  polar covalent bond A difference of > 1.6  ionic bond

H O H H2OH2O ++ ++ –– Bonds in Water Oxygen electronegativity = 3.44 Hydrogen electronegativity = 2.2 Difference 3.44 – 2.2 = 1.24 Bond Type  Polar covalent In a water molecule the oxygen is slightly negatively charged.

Inter- Molecular Interactions The properties of molecules can influence their interactions with other molecules. These are weaker bonds than intramolecular bonds. 1.hydrogen bonding 2.dipole-dipole interactions 3.London/dispersion force

Water: A special molecule a) Hydrogen bonding Effects: cohesion, adhesion, surface tension. More energy is needed to break hydrogen bonds than other intermolecular bonds, which gives water a high specific heat capacity. b) Density Effects: Ice is less dense so it floats, insulating water underneath.

Water: A special molecule c) Polar nature of the bond Effects: as a solvent, water allows polar molecules and ionic compounds to dissolve due to water’s polarity d) Dissociation of intramolecular bonds Effects: 1 in 10 7 water molecules dissociates to form H + and OH - ions. This is a pH of 7 = NEUTRAL.

Functional Groups Functional groups are parts of larger molecules. They greatly influence biological reactivity.

Functional Groups Hydroxyl – alcohols Carboxyl – acids Amino – bases Carbonyl – aldehydes and ketones

Functional Groups One biologically important functional group missing from this list is sulfhydryl, which contains sulphur. The name of molecules with this functional group is thiol. The ‘R’ represents the rest of the molecule.

Functional Groups Sulphur forms relatively strong intermolecular bonds with other sulphurs. This is important to forming the 3D structure of proteins.

Extra slides for students without chemistry background

LE 4-10aa STRUCTURE (may be written HO—) NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Ethanol, the alcohol present in alcoholic beverages FUNCTIONAL PROPERTIES Is polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).

LE 4-10ab STRUCTURE NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton EXAMPLE Acetone, the simplest ketone A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Aldehydes if the carbonyl group is at the end of the carbon skeleton Acetone, the simplest ketone Propanal, an aldehyde FUNCTIONAL PROPERTIES

LE 4-10ac STRUCTURE NAME OF COMPOUNDS Carboxylic acids, or organic acids EXAMPLE Has acidic properties because it is a source of hydrogen ions. Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H + ) tend to dissociate reversibly; for example, Acetic acidAcetate ion In cells, found in the ionic form, which is called a carboxylate group.

LE 4-10ba STRUCTURE NAME OF COMPOUNDS Amine EXAMPLE Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES Acts as a base; can pick up a proton from the surrounding solution: (nonionized) Ionized, with a charge of 1+, under cellular conditions Glycine (ionized)

LE 4-10bb STRUCTURE (may be written HS—) NAME OF COMPOUNDS Thiols EXAMPLE Ethanethiol FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).

LE 4-10bc STRUCTURE NAME OF COMPOUNDS Organic phosphates EXAMPLE Glycerol phosphate FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules.