12-01: Functional Groups and Linkages

  • Most of a living organism is water
  • The remaining amount of “stuff” in an organism falls into 4 main categories:

  
  1. Carbohydrates
  2. Lipids
  3. Proteins
  4. Nucleic Acids

Biochemistry

  • Many cellular molecules are complex and can be made up of thousands of atoms
  • These molecules are made by stringing together many smaller units → Single units are called monomers, multiple units are called polymers
  • Anabolic reactions: build up substances
  • Catabolic reactions: break down substance
  • Both catabolic and anabolic reactions occurring in an organism: metabolism

Intramolecular bonds: bonds within a molecule

3 types of intramolecular bonds

  • Covalent bonds
      * 2 atoms share electrons (e-) → 2 non metals
  • Ionic bonds
      * 1 atom loses an e- and 1 gains an e-
  • Polar covalent bonds
      * Sharing the e- less fairly

Electronegativity (EN): the strength in which an atom attracts e- → how aggressive it is

The type of intramolecular bond is distinguished by a difference in electronegativity (∆EN)

  • Covalent: ∆EN < 0.4 → share equally
  • Polar covalent: ∆EN = 0.5-1.7
  • Ionic: ∆EN > 1.7 → atom with greater EN takes e- from atom with lesser EN and both become charged

Polar Covalent Bonds

  • One atom has a stronger hold on e- they share
  • One end of the molecule gets slightly positively charged and one end gets slightly negatively charged

δ+ → one end gets + charge (weaker EN)

δ- → one end gets - charge (stronger EN)

This influences what will be attracted and how things will biologically interact

Water is polar → has polar covalent intramolecular bonds

  • Because of Oxygen (O)’s EN, e- tend to spend more time near the O atom than near the Hydrogen (H) atoms
  • The unequal sharing e- creates a slight difference in the charge between the ends/poles of the molecule
  • the O end is δ- and the H ends are δ+
      * Due to its polarity, water forms H bonds with itself
        * Very weak bonds, but many of which come together and become very strong together

Water also forms bonds through….

  • Cohesion: water molecules are attracted to other water molecules
  • Adhesion: water is a polar molecule and thus attracts other polar molecules

Intermolectular forces: bonds between molecules

  • ==London dispersion forces==: very weak attraction between molecules, even non polar ones. Increases with molecule size
  • @@Dipole dipole attraction@@: attractive force between 2 polar molecules
  • @@H bonding:@@ special kind of dipole dipole attraction; between 2 polar molecules with Hydrogen bonded to N, O, or F

Carbon - the element of life

  • Backbone of nearly every biological molecule (except for water)
  • Organic compound: compound that contains carbon-hydrogen bonds (may also contain other elements like O, N, etc) and is often found in organisms
  • ^^C and H form a non polar bond so hydrocarbons are non polar^^
      * Polarity can be achieved by adding other atoms called functionalgroupsfunctional groups (FGs)

- Functional Groups -

  • Molecules interact with each other at specific regions of their molecules (^^changes the dynamic of the molecule that allow it it interact differently^^)
  • Used to classify molecule types
  • After a reaction between 2 molecules’ functional groups, a linkage will be formed
      * Monomers link to form polymers. This happens because of FGs reacting

Classifying FGs: if it has the FG, then it is classified that certain way

 

Types of Reactions

2 types:

1. Hydrolysis

  • Rupture → use of water to rupture, break down
  • Catabolic
      * Used to split larger molecules apart
  • Water is required and it is used up → it is a reactant

 

2. Dehydration synthesis (condensation)

  • Condenses smaller particles into larger ones
  • Anabolic
      * Used to build up molecules
  • Water is released → it is a product

 

Linkages that form in dehydration synthesis reactions

Ether Linkages

(glycosidic link between sugars, when it occurs between sugar molecules)

  • Between %%2 hydroxyl groups%% (alcohols)
  • Used in carbohydrates
  • Forms the pattern COC

 

Ester Linkages

  • Between a %%hydroxyl and a carboxyl group%% (when they react)
  • Used in triglycerides
  • Forms the pattern OCO

 

The double bond indicates that it is an ester linkage

Phosphate Ester Linkages

  • Between hydroxyl FGs (first) and phosphate FGs (second)
  • Used in phospholipids and nucleic acid, which instructs the cells, DNA and RNA
  • Forms the pattern OPO

 

Peptide Linkages

  • Between carboxyl FGs (first) and amino FGs (second)
  • Links amino acids together
  • Forms the pattern OCNH