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

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