The Foundations of Biochemistry (Lec 1)

Question 1

Molecular Complementarity

Answer 1

Enables proteins with complimentary shapes and chemical properties to form biomolecular interactions

Question 2

Chemical Building Blocks

Answer 2

Small molecule building blocks form larger cellular structures and polymers

Question 3

Chemical Equilibrium

Answer 3

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

Question 4

Chemical Bond Energy

Answer 4

Energy driving many cellular activities is derived from hydrolysis of the phosphoanhydride bond in ATP

Question 5

Molecular Hierarchy of Structure

Answer 5

Monomeric Units (subunits) -> Macromolecules -> Supramolecular complexes -> The cell/organelles

Question 6

Isomer

Answer 6

Molecules that share the same chemical formula but have a different arrangement of atoms

Question 7

Stereoisomer

Answer 7

Isomers that have different physical properties

Question 8

Geometric

Answer 8

Isomers that have different physical and chemical properties

Question 9

Enantiomers

Answer 9

Isomers that have identical physical properties and react identically with achiral reagents (mirror images)

Question 10

Diastereomers

Answer 10

Have different physical and chemical properties (non-mirror images)

Question 11

Cis.

Answer 11

Isomers with Cis- indicates that the functional groups are on the same side of the carbon chain

Question 12

Trans.

Answer 12

Isomers with Trans- indicates that functional groups are on opposing sides of the carbon chain

Question 13

Biomolecule Interactions are…

Answer 13

SPECIFIC!

Macromolecules fold into 3D structures with unique binding pockets, allowing only certain molecules to fit in and bind

Question 14

How to Speed Up Reactions

Answer 14

1. Increase temp.
2. Increase reactant concentration
3. Change the reaction by coupling with a more efficient one
4. Lower activation barrier through catalysis

Question 15

Unfavourable Reactions

Answer 15

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).

Question 16

Favourable Reactions

Answer 16

Releases energy (exergonic)
- Breakdown of some molecules

Question 17

Energy Coupling

Answer 17

Chemical coupling of exergonic and endergonic reactions allows otherwise unfavourable reactions

Question 18

Catalysis

Answer 18

A catalyst is a compound that increases the rate of a chemical reaction by:
- lowering the activation energy ΔG‡

Question 19

Feedback Inhibition

Answer 19

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

Question 20

Central Dogma of Biochem

Answer 20

Gene on DNA strand -> transcribed into Messenger RNA -> translated into Polypeptide Chain -> folding of polypeptide chain into Native Structure

Question 21

Hydrogen Bonds

Answer 21

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

Question 22

Water as a Solvent

Answer 22

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)

Question 23

Amphipathic

Answer 23

Molecule consisting of both polar and non-polar functional groups

Question 24

Non-covalent Interactions: Ionic Interactions

Answer 24

Electrostatic interactions between permanently charged species, or between the ion and a permanent dipole

Question 25

Non-covalent Interactions: Dipole Interactions (H-Bonds)

Answer 25

Electrostatic interactions between uncharged but polar molecules that produce alpha helices and beta sheets

Question 26

Non-covalent Interactions: Van der Waals Interactions

Answer 26

Weak interactions between all atoms, regardless of polarity. Attractive (London dispersion) and repulsive (Steric repulsion) component

Question 27

Non-covalent Interactions: Hydrophobic Effect

Answer 27

Complex phenomenon associated with the ordering of water molecules (aqueous solution) around nonpolar substances

Question 28

Hydrophobic Effect favors Ligand Bonding

Answer 28

Binding sites in enzymes and receptors are usually hydrophobic, and such sites allow easy binding as water is displaced and entropy increases

Question 29

Origin of Hydrophobic Effect

Answer 29

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

Question 30

Ionization of Water (H2O -> H+ and OH-)

Answer 30

(H2O -> H+ and OH-)

O-H bonds are polar and can dissociate heterolytically, producing a proton (H+ ion) and a Hydroxide ion (OH-)

Question 31

Proton Hydration

Answer 31

Protons do not exist free in solution, they are rapidly hydrated to form hydronium ions (H3O+).

Question 32

Proton Hopping

Answer 32

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

Question 33

pH

Answer 33

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.

Question 34

Dissociation of Weak Electrolytes

Answer 34

Weak electrolytes dissociate only partially in water, the extent of dissociation is determined by the acid dissociation constant Ka.

Question 35

pKa Measures Acidity

Answer 35

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)

Question 36

pH = pKa

Answer 36

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