The Chemical Nature of Life

Molecules May Change Their Shape

  • 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

  • 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

  • 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 and Nonpolar Covalent Bonds

  • 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 Bonds

  • 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

Other Noncovalent Bonds

  • 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

Weak Chemical Bonds

  • 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

  • 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

Effects of pH

  • 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

Carbon Isomers

  • 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

  • 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

Lipids

  • 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

Phospholipids

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