Chapter 1

Question 1

DNA types

Answer 1

Alpha helixes

Beta sheets

Question 2

Bonds between nucleotides

Answer 2

Hydrogen bonds

Question 3

Biological Relevance of Hydrogen Bonds

Answer 3

Hydrogen bonds between

• alcohol and water
• ketone and water
• peptide bonds
• DNA bases

Question 4

Water is a good solvent for charged and polar substances like

Answer 4

Amino acids and peptides
Small alcohols
Carbohydrates

Question 5

Water is a poor solvent for non polar solvents like:

Answer 5

Nonpolar gases
Aromatic moieties
Aliphatic chains

Question 6

Examples of Noncovalent Interactions

Answer 6

Hydrogen bonds
Peptide bonds
Ionic interactions
Hydrophobic interactions
Van deer waals interactions

Question 7

Van der Waals interactions

Answer 7

Attractive force (London) due to polarizability
Repulsive force (Steric) due to atom size

Attraction dominates at longer distances
-There is a minimum energy distance because very strong repulsive forces become dominant because the outer electron clouds of the two atoms overlap

Question 8

Biochemical Significance of Van der Waals Interactions

Answer 8

Occur where atoms are near each other
Important
-Determine steric complementarity
-Stabilizes biological macromolecules (stacking in DNA)
-Facilitates binding in polarizable ligand

Question 9

The Hydrophobic Effect

Answer 9

One main factors behind:

• protein folding
• protein-protein association
• formatting of lipid micelles
• binding of steroid hormones to their receptors

Question 10

Dissociation or Weak Electrolytes

Answer 10

Extent of dissociation is determined by the acid dissociation constant Ka

Question 11

Pka measures acidity

Answer 11

pKa = -log Ka

• strong acid -> large Ka -> small pKa
• when pH=pKa, the concentration of the deprotonated form of the molecules is equal to the concentration of protonated form.

Question 12

Biological Buffer Systems

Answer 12

Maintenance of intracellular pH is vital to all cells

• Enzyme catalyzed reactions have optimal pH
• Solubility of polar molecules depends on H-bond donors and acceptors
• Equilibrium between CO2 gas and dissolved HCO-3 depends on pH

Question 13

Buffer systems in vivo are mainly based on

Answer 13

• Phosphate, concentration in millimolar range
• bicarbonate, important for blood plasma
• histidine, efficient buffer at neutral pH

Question 14

Buffer systems in vitro are often based on sulfonic acids of cyclin amines

Answer 14

• HEPES
• PIPES
• CHES