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