The Chemical Nature of Life

Atoms combine to form a molecule with three dimensional shape
The shape is determined by the arrangement and number of bonds between atoms
Angles that form between atoms give molecules specific shapes
Covalent bonds are not rigid and rotation around single covalent bonds allows molecules to change shape
There’s rotation in the atoms that make up a molecule with single bonds
Atoms in molecules with double bonds are linear and don’t rotate

Covalent bonds: formed when the atoms of a molecule share electrons * The angles formed are specific and defined * Have definite and predictable shapes * Not easily broken under normal biological conditions of temperature and pressure
Polar and nonpolar covalent bonds * Determines the behavior of the molecule * Nonpolar covalent bond: equal distribution of charge so molecule doesn’t feel the need to interact with other molecules, unlike polar covalent bonds * Polarity determines whether a molecule is hydrophobic or hydrophilic, which determines its location in proteins

Carbon has 4 electrons in its outer shell
It can make up to four bonds * Usually single or double bonds
Carbon can form nonpolar or polar bonds * Molecules with polar bonds are water soluble * Molecules with nonpolar bonds (like hydrocarbons) are not very water soluble

Polar covalent bonds are important because these kinds of bonds allow the formation of another kind of weak bond called a hydrogen bond.
Molecules consisting of mainly nonpolar covalent bonds are hydrophobic.
Hydrogen bonds are very weak in comparison to covalent bonds, so it takes very little energy to break in comparison * Hydrogen bonds keep the 2 strands of DNA together which is better for DNA replication because they need to be separated

Hydrogen bond: force of attraction between a hydrogen in a polar molecule and electronegative portion in another molecule * Has only about 5% of the strength of a covalent bond * When multiple hydrogen bonds can form within a molecule or between 2 molecules, the bond can be sufficiently strong and stable
Examples of the role of hydrogen bonds include * Holding 2 strands of DNA together * Holding polypeptides together * Assist enzymes in substrate in bonds * Help antibodies bind to their substrate

Ionic bonds: electrons are removed from one atom and transferred to another
Van der Waals Interactions: weak, nonspecific attractive force * Requires atoms or molecules to be close together * if electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charges * Van der Waals interactions are attractions between molecules that are close together as a result of these charges

Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules
Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other * a molecule’s shape is usually very important to its function * A molecule’s shape is determined by the positions of its atoms’ valence electrons
In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes

Water has many important functions in living organisms: * Participates in chemical reactions (hydrolysis or condensation) * Provides force or support * Removes toxic waste components * Evaporative cooling (ex: sweat) * Cohesion and adhesion * Surface tension * Lubrication
Specific heat: the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC * The specific heat of water is 1 cal/g/ºC * Water resists changing its temperature because of its high specific heat * Water’s high specific heat can be traced to hydrogen bonding * Heat is absorbed when hydrogen bonds break * Heat is released when hydrogen bonds form * The high specific heat of water minimizes temperature fluctuations to within limits that permit life

The pH of a solution can affect * The shapes and functions of molecules * The rates of many chemical reactions * The ability of two molecules to bind to each other (shape of the active site could be altered) * The ability of ions or molecules to dissolve in water

Isomers: compounds with the same molecular formula but different structures and properties
Geometric isomers * Require double bond * Cis or trans
Enantiomers * Have asymmetric carbon * Never superimposable * Have biological relevance * all the atoms the carbon is bonded to are different

Functional groups: groups of atoms with special chemical features that are functionally important
Each type of functional group exhibits the same properties in all molecules in which it occurs

Composed predominantly of hydrogen and carbon atoms
Defining feature of lipids is that they are nonpolar and therefore very insoluble in water (hydrophobic)
Include fats, phospholipids, steroids, and waxes
Lipids comprise about 40% of the organic matter in the average human body

Formed from glycerol, two fatty acids and a phosphate group
Phospholipids are amphipathic molecules * Phosphate head: polar / hydrophilic * Fatty acid tail: nonpolar / hydrophobic

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