Biochemistry Chapter 2

Name the 5 hierarchical levels of molecules important in biological systems

1. Inorganic precursors (CO2, H2O, NH3, N2)

2. Metabolites (Pyruvate, Citrate, Succinate)

3. Building blocks (Amino acids, Nucleotides)

4. Macromolecules (Proteins, Nucleic acids)

5. Supramolecular Complexes (Ribosomes, Cytoskeleton)

Properties of molecules is based on what?

• Composition

• Covalent structure

• Bonding and molecular geometry

What space will electrons occupy?

Space with minimum repulsion. As far away from each other as possible.

Chemical bonds allow what?

The sharing of electrons between the nuclei of the two bonded atoms. Can be shared equally or unequally.

What does degree of electron sharing determine about a bond?

• Strength of bond

• Energy associated with the bond

Define electronegativity

The ability of an atom within a molecule to draw electrons towards itself. When EN is equal between atoms electron is equally shared.

Explain the difference between polar and non-polar covalent bonds.

Non-polar, electrons are shared equally. H2.

Polar, electrons reside closer to nucleus with greater ability to attract them. HCl.

Define hydrogen bond in relation to water.

Electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another.

What properties of water are higher due to hydrogen bonding?

• Melting point

• Boiling point

• Heat of vaporization

• Surface tension

Are H bonds shorter or longer than covalent?

Longer

What can be said about the strength and lifetime of H-bonds?

BDE = ~23kJ/mol in H2O

Polar bonds

10% covalent, 90% electrostatic

Strong dipole-dipole or charge-dipole interactions

Strongest when bonded molecules allow for linear bonding patterns

Bond lifetime in liquid is 1-20 picoseconds

When one H bond breaks, another forms

Why are H bonds biologically important?

• Sources of unique properties of water

• Structure and function of proteins

• Structure and function of DNA

• Structure and function of polysaccharides

• Binding of substrates to enzymes

• Binding of hormones to receptors

• Matching of mRNA and tRNA

H’s bonded to what atoms can participate in hydrogen bonding?

F, O, N (Fluorine, Oxygen, Nitrogen)

Phase changes from solid to liquid and liquid to gas for water are spontaneous but endothermic. What must increase to drive these changes?

Entropy (S)

Up to how many H bonds can water form in its liquid state?

3

Up to how many H bonds can water form in its solid state?

4

What is the result of water being able to form more H bonds in its solid state?

A lower density than liquid water. Ice floats.

Define hydrophilic

Compounds that dissolve easily in water; generally charged or polar compounds

Define hydrophobic

Compounds that do not dissolve easily in water; nonpolar molecules such as lipids and waxes

Define amphipathic

A compound that contains regions that are polar (or charged) and regions that are nonpolar

Water is a good solvent for what types of substances?

Charge and polar

• Amino acids

• Peptides

• Small alcohols

• Carbohydrates

Water is a poor solvent for what types of substances?

Nonpolar

• Nonpolar gases

• Aromatic moieties

• Aliphatic chains

How is force of ionic interactions in solution calculated?

Q = Magnitude of charges

r = distance between charged group

E = dielectric constant of the solvent (Water at 25 degree Celsius = 78.5)

Over what distance do ionic attractions or repulsions operate?

10-40 nm

How does a high dielectric constant affect attraction between oppositely charged ion in a salt crystal?

Reduces it.

As a crystal lattice is dissolved what happens to entropy?

It increases

How do strong electrostatic interactions between the solvated ions and water molecules affect the energy of the system?

Lowers it.

How does water dissolve most crystalline salts?

By hydrating their component ions. Ionic charges are partially neutralized and electrostatic attractions needed for lattice formation are weakened.

What types of non-covalent interactions exist?

• Ionic interactions

• Dipole interactions

• van der Waals interactions

• Hydrophobic effects

What two components make up van der Waals interactions and what do they depend on?

Attractive force (London dispersion) depends on polarizability

Repulsive force (Steric repulsion) depends on size of atoms

Explain the importance of van der Waals interactions

• Universal occur between any two atoms near each other

• Weak individually; easily broken and reversible

• Determines steric complementarity

• Stabilizes biological macromolecules (base stacking in DNA)

• Facilitates binding of polarizable ligands

What is the hydrophobic effect and what biological processes is it the driving force for?

Refers to the association or interaction of nonpolar molecules or components of molecules in the aqueous solution.

Main factor behind:

• Protein folding

• Protein-protein association

• Formation of lipid micelles

• Binding of steroid hormones to their receptors

Water surrounding nonpolar solutes has lower or higher entropy?

Lower

Micelle formation is thermodynamically favored why?

The ordered shell of H2O molecules is minimized and entropy is increased