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

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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

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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

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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

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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)

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

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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

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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

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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

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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 functional groups (FGs)

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- 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

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

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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

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Linkages that form in dehydration synthesis reactions

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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

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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

  

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Peptide Linkages

• Between carboxyl FGs (first) and amino FGs (second)

• Links amino acids together

• Forms the pattern OCNH

  

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