Introduction & basic chemistry
• Define biochemistry and its role in living organisms
• The four major classes of biomolecules (carbohydrates, lipids, proteins, & nucleic acid)
Biochemistry: the study of chemical substances and vital processes occurring in a living system
Biomolecule: an organic compound normally present as an essential component of living organisms
Fig. 13-28 pg.497 KEGG Metabolic Map
Types of Biomolecules:
1) Carbohydrates (sugars)
● Energy & energy storage (glucose, glycogen(
● Structure (cellulose)
● Cell recognition
● Components of DNA & RNA
2) Proteins
● Catalysts (enzymes) (Alcohol Dehydrogenase)
● Transport (Hemoglobin)
● Structure (Keratin)
● Signalling (Insulin)
● Defense (Antibodies)
● Storage (Ferritin)
3) Lipids (Fats)
● Energy / Energy Storage (fatty acid triglycerides)
● Barriers (membranes, phospholipids)
● Signalling (steroid hormones)
● Insulation (blubber)
4) Nucleic Acids
● Information storage (DNA/RNA)
● Catalysis (Ribozymes)
● Energy Transfer
● Components of Cofactors (NAD+, FAD)
Atoms and bonding
• Types of molecular interactions in biochemistry:
A) Atoms and Bonding:
● Most biomolecules are composed of the following elements: Carbon, Hydrogen, Oxygen,
Nitrogen, Phosphorus, Sulfur
● Interested how the molecules are made up and how they interact with themselves and each other
● Different types of interactions are known as Bonding
5 Major Types of Bonding:
1) Covalent Bonding
● Sharing of electrons (e-) between 2 adjacent atoms
● Covalent bonds are drawn as solid lines
Fig. 1-12 pg.11
● Not easily reversible (i.e. stable)
, ● High energy *
● Small bond length * relative to other interactions
● Covalent bonds bind atoms together to from the biomolecules
● Usually the strongest type of bonding “4 Adenine”
Geometry of Carbon Bonding:
● When carbon has 4 single bonds it adopts a tetrahedral structure with bond angle of 109°
with free rotation about the bonds.
Fig. 1-13 A & B pg.11
● When carbon has a double bond, it adopts a trigonal planar structure with bond angles at
120° there is no rotation about the double bond and a series of atoms are locked in a
plane.
● The remaining types of interactions are Electrostatic (with the exception of Hydrophobic
Interactions)
● They allow the various biomolecules to interact with themselves and each other
Ex) DNA structure & replication, protein folding and substrate binding
* note: Fig 1-13 pg.15 is a reference for the common functional groups used in Biochemistry
2) Ionic Interactions of 2 Charges Atoms based on Coulomb's Law
● 8 charges on the atom
𝑞1𝑞2
● 𝐹 = 2
ε𝑟
● 𝐹 = 𝑓𝑜𝑟𝑐𝑒 𝑜𝑓 𝑡ℎ𝑒 𝑖𝑛𝑡𝑒𝑟𝑎𝑐𝑡𝑖𝑜𝑛
● ε = 𝑑𝑖𝑒𝑙𝑒𝑐𝑡𝑟𝑖𝑐 𝑐𝑜𝑛𝑠𝑡𝑎𝑛𝑡 (𝑡𝑎𝑘𝑒𝑠 𝑖𝑛𝑡𝑜 𝑎𝑐𝑐𝑜𝑢𝑛𝑡 𝑡ℎ𝑒 𝑚𝑒𝑑𝑖𝑢𝑚 𝑡ℎ𝑒 𝑎𝑡𝑜𝑚𝑠 𝑎𝑟𝑒 𝑖𝑛)
● 𝑟 = 𝑑𝑖𝑠𝑡𝑎𝑛𝑐𝑒
Note: water has high dielectric constant
3) Hydrogen Bond
● A hydrogen atom is part way shared by two electronegative atoms
Fig. 2-1b pg.44
● Requires a hydrogen donor (which the hydrogen is covalently bound to) and a hydrogen
acceptor. Both are usually Oxygen or Nitrogen (sometimes Sulfur). This is a special form
of an Electrostatic Interaction
● The hydrogen donor is electronegative and tends to pull electrons away from the
hydrogen.
−
● Result: electronegative donor becomes partly negatively charged (δ )
+
● Hydrogen becomes partly positively charged (δ )
, −
● The acceptor is also electronegative and develops a δ (partial negative charge)
+ −
● It has to have a lone pair of electron the δ charged H is attracted to the δ acceptor and
a hydrogen bond is formed.
−10
● H-bonds are weak 4-13 KJ/mole and longer 1.5 - 2.6 Å (Å = 10 ) than covalent bonds
Fig 2-4 pg.45 shows H bonding in Gases pairing in DNA.
4) Van der Waals Interaction (London Dispersion)
● Attraction of any 2 molecules
● Also a specialized form of electrostatic interaction
● At any given time, the charge distribution around an atom is not symmetric
● This asymmetry causes complementary symmetric or other atom resulting in the 2 atoms
being attracted to each other
Fig 1-10 BIOC 6th Ed
● The attraction increases until the electron clouds start to overlap and repel
● Van der waals contact distance is the distance of maximal attraction of the two atoms
● Has small energies of 2-4 KJ/moles
Fig 1-14 see slide showing the distance between base pairs in DNA is Van der Waals
contact distance.
5) Hydrophobic Interaction / Effect
● Special type of interaction
● Will discuss more shortly
Water
• Structure
• Role in Biomolecular interactions
B) Water:
● Almost all biochemical reactions occur in aqueous solvent (in water)
● Water has a big effect on these reactions and interactions.
● Water has a bent shape, making the molecule polar and capable of forming multiple hydrogen
bonds. Because of this, water is very cohesive, that is, water molecules can form H-bonds with
each other.
Fig. 2-2 pg.45 structure of ice showi9ng multiple H bonds
● Water is an excellent solvent for polar or charged molecules
Hydrophilic: (water loving) molecules or groups that are soluble in molecules.
• Define biochemistry and its role in living organisms
• The four major classes of biomolecules (carbohydrates, lipids, proteins, & nucleic acid)
Biochemistry: the study of chemical substances and vital processes occurring in a living system
Biomolecule: an organic compound normally present as an essential component of living organisms
Fig. 13-28 pg.497 KEGG Metabolic Map
Types of Biomolecules:
1) Carbohydrates (sugars)
● Energy & energy storage (glucose, glycogen(
● Structure (cellulose)
● Cell recognition
● Components of DNA & RNA
2) Proteins
● Catalysts (enzymes) (Alcohol Dehydrogenase)
● Transport (Hemoglobin)
● Structure (Keratin)
● Signalling (Insulin)
● Defense (Antibodies)
● Storage (Ferritin)
3) Lipids (Fats)
● Energy / Energy Storage (fatty acid triglycerides)
● Barriers (membranes, phospholipids)
● Signalling (steroid hormones)
● Insulation (blubber)
4) Nucleic Acids
● Information storage (DNA/RNA)
● Catalysis (Ribozymes)
● Energy Transfer
● Components of Cofactors (NAD+, FAD)
Atoms and bonding
• Types of molecular interactions in biochemistry:
A) Atoms and Bonding:
● Most biomolecules are composed of the following elements: Carbon, Hydrogen, Oxygen,
Nitrogen, Phosphorus, Sulfur
● Interested how the molecules are made up and how they interact with themselves and each other
● Different types of interactions are known as Bonding
5 Major Types of Bonding:
1) Covalent Bonding
● Sharing of electrons (e-) between 2 adjacent atoms
● Covalent bonds are drawn as solid lines
Fig. 1-12 pg.11
● Not easily reversible (i.e. stable)
, ● High energy *
● Small bond length * relative to other interactions
● Covalent bonds bind atoms together to from the biomolecules
● Usually the strongest type of bonding “4 Adenine”
Geometry of Carbon Bonding:
● When carbon has 4 single bonds it adopts a tetrahedral structure with bond angle of 109°
with free rotation about the bonds.
Fig. 1-13 A & B pg.11
● When carbon has a double bond, it adopts a trigonal planar structure with bond angles at
120° there is no rotation about the double bond and a series of atoms are locked in a
plane.
● The remaining types of interactions are Electrostatic (with the exception of Hydrophobic
Interactions)
● They allow the various biomolecules to interact with themselves and each other
Ex) DNA structure & replication, protein folding and substrate binding
* note: Fig 1-13 pg.15 is a reference for the common functional groups used in Biochemistry
2) Ionic Interactions of 2 Charges Atoms based on Coulomb's Law
● 8 charges on the atom
𝑞1𝑞2
● 𝐹 = 2
ε𝑟
● 𝐹 = 𝑓𝑜𝑟𝑐𝑒 𝑜𝑓 𝑡ℎ𝑒 𝑖𝑛𝑡𝑒𝑟𝑎𝑐𝑡𝑖𝑜𝑛
● ε = 𝑑𝑖𝑒𝑙𝑒𝑐𝑡𝑟𝑖𝑐 𝑐𝑜𝑛𝑠𝑡𝑎𝑛𝑡 (𝑡𝑎𝑘𝑒𝑠 𝑖𝑛𝑡𝑜 𝑎𝑐𝑐𝑜𝑢𝑛𝑡 𝑡ℎ𝑒 𝑚𝑒𝑑𝑖𝑢𝑚 𝑡ℎ𝑒 𝑎𝑡𝑜𝑚𝑠 𝑎𝑟𝑒 𝑖𝑛)
● 𝑟 = 𝑑𝑖𝑠𝑡𝑎𝑛𝑐𝑒
Note: water has high dielectric constant
3) Hydrogen Bond
● A hydrogen atom is part way shared by two electronegative atoms
Fig. 2-1b pg.44
● Requires a hydrogen donor (which the hydrogen is covalently bound to) and a hydrogen
acceptor. Both are usually Oxygen or Nitrogen (sometimes Sulfur). This is a special form
of an Electrostatic Interaction
● The hydrogen donor is electronegative and tends to pull electrons away from the
hydrogen.
−
● Result: electronegative donor becomes partly negatively charged (δ )
+
● Hydrogen becomes partly positively charged (δ )
, −
● The acceptor is also electronegative and develops a δ (partial negative charge)
+ −
● It has to have a lone pair of electron the δ charged H is attracted to the δ acceptor and
a hydrogen bond is formed.
−10
● H-bonds are weak 4-13 KJ/mole and longer 1.5 - 2.6 Å (Å = 10 ) than covalent bonds
Fig 2-4 pg.45 shows H bonding in Gases pairing in DNA.
4) Van der Waals Interaction (London Dispersion)
● Attraction of any 2 molecules
● Also a specialized form of electrostatic interaction
● At any given time, the charge distribution around an atom is not symmetric
● This asymmetry causes complementary symmetric or other atom resulting in the 2 atoms
being attracted to each other
Fig 1-10 BIOC 6th Ed
● The attraction increases until the electron clouds start to overlap and repel
● Van der waals contact distance is the distance of maximal attraction of the two atoms
● Has small energies of 2-4 KJ/moles
Fig 1-14 see slide showing the distance between base pairs in DNA is Van der Waals
contact distance.
5) Hydrophobic Interaction / Effect
● Special type of interaction
● Will discuss more shortly
Water
• Structure
• Role in Biomolecular interactions
B) Water:
● Almost all biochemical reactions occur in aqueous solvent (in water)
● Water has a big effect on these reactions and interactions.
● Water has a bent shape, making the molecule polar and capable of forming multiple hydrogen
bonds. Because of this, water is very cohesive, that is, water molecules can form H-bonds with
each other.
Fig. 2-2 pg.45 structure of ice showi9ng multiple H bonds
● Water is an excellent solvent for polar or charged molecules
Hydrophilic: (water loving) molecules or groups that are soluble in molecules.
