The Foundations of Biochemistry (Lec 1) Flashcards
Molecular Complementarity
Enables proteins with complimentary shapes and chemical properties to form biomolecular interactions
Chemical Building Blocks
Small molecule building blocks form larger cellular structures and polymers
Chemical Equilibrium
Chemical reactions are reversible. The ratio of forward (kf) and reverse (kr) reaction rate constants, reflects the relative amount of products and reactants at equilibrium
Chemical Bond Energy
Energy driving many cellular activities is derived from hydrolysis of the phosphoanhydride bond in ATP
Molecular Hierarchy of Structure
Monomeric Units (subunits) -> Macromolecules -> Supramolecular complexes -> The cell/organelles
Isomer
Molecules that share the same chemical formula but have a different arrangement of atoms
Stereoisomer
Isomers that have different physical properties
Geometric
Isomers that have different physical and chemical properties
Enantiomers
Isomers that have identical physical properties and react identically with achiral reagents (mirror images)
Diastereomers
Have different physical and chemical properties (non-mirror images)
Cis.
Isomers with Cis- indicates that the functional groups are on the same side of the carbon chain
Trans.
Isomers with Trans- indicates that functional groups are on opposing sides of the carbon chain
Biomolecule Interactions are…
SPECIFIC!
Macromolecules fold into 3D structures with unique binding pockets, allowing only certain molecules to fit in and bind
How to Speed Up Reactions
- Increase temp.
- Increase reactant concentration
- Change the reaction by coupling with a more efficient one
- Lower activation barrier through catalysis
Unfavourable Reactions
Requires energy (endergonic)
- A reaction might be thermodynamically unfavorable (ΔG°> 0) and requires work and energy for order
- A metabolic reaction might have too high an energy barrier (ΔG‡ > 0).
Favourable Reactions
Releases energy (exergonic) - Breakdown of some molecules
Energy Coupling
Chemical coupling of exergonic and endergonic reactions allows otherwise unfavourable reactions
Catalysis
A catalyst is a compound that increases the rate of a chemical reaction by:
- lowering the activation energy ΔG‡
Feedback Inhibition
In a process where multiple enzymes are at work, the product (or excess of a product) of the final enzyme inhibits an enzyme earlier in the cycle
Central Dogma of Biochem
Gene on DNA strand -> transcribed into Messenger RNA -> translated into Polypeptide Chain -> folding of polypeptide chain into Native Structure
Hydrogen Bonds
Strong dipole-dipole bond that arise between a covalently bound Hydrogen atom and a lone pair of electrons
- Stronger bonds formed when atoms are in line
- Weaker when atoms are bent at the bonds
Water as a Solvent
Good solvent for charged and polar substances:
– amino acids and peptides
– small alcohols
– carbohydrates
Poor solvent for nonpolar substances:
– nonpolar gases
– aromatic moieties
– aliphatic chains (lipids)
Amphipathic
Molecule consisting of both polar and non-polar functional groups
Non-covalent Interactions: Ionic Interactions
Electrostatic interactions between permanently charged species, or between the ion and a permanent dipole
Non-covalent Interactions: Dipole Interactions (H-Bonds)
Electrostatic interactions between uncharged but polar molecules that produce alpha helices and beta sheets
Non-covalent Interactions: Van der Waals Interactions
Weak interactions between all atoms, regardless of polarity. Attractive (London dispersion) and repulsive (Steric repulsion) component
Non-covalent Interactions: Hydrophobic Effect
Complex phenomenon associated with the ordering of water molecules (aqueous solution) around nonpolar substances
Hydrophobic Effect favors Ligand Bonding
Binding sites in enzymes and receptors are usually hydrophobic, and such sites allow easy binding as water is displaced and entropy increases
Origin of Hydrophobic Effect
Dispersion of lipids in H2O
- non-polar tails of lipids exposed to ordered water molecules
- entropy of system decreases
Clustering of lipids in H2O
- non-polar portions aggregate so that fewer water molecules are ordered
- increases entropy of system
Ionization of Water (H2O -> H+ and OH-)
(H2O -> H+ and OH-)
O-H bonds are polar and can dissociate heterolytically, producing a proton (H+ ion) and a Hydroxide ion (OH-)
Proton Hydration
Protons do not exist free in solution, they are rapidly hydrated to form hydronium ions (H3O+).
Proton Hopping
Protons hop between series of hydrogen-bonded water molecules. As a Hydronium ion (H3O+) loses a proton (H+), a water molecule (H2O) gains one. Results in rapid net movement of protons over a long distance
pH
pH is defined as the negative logarithm of the hydrogen ion concentration (pH = -log[H+]). In neutral solution, [H+] = [OH–] and the pH is 7.
Dissociation of Weak Electrolytes
Weak electrolytes dissociate only partially in water, the extent of dissociation is determined by the acid dissociation constant Ka.
pKa Measures Acidity
pKa is defined as the negative log of the dissociation constant. A lower pKa value indicates a stronger acid (acid more fully dissociated in water)
pH = pKa
At pH = pKa, there is a 50:50 mixture of acid and anion forms of the compound. Buffering capacity of acid/anion system is greatest at pH = pKa
