Lecture 1: Chemical Interactions in Biological Systems

Question 1

Water is found in

Answer 1

Typical eukaryotic cell: 65-70%
Human body: 65%
Reactions occur within a solvent; major solvent in cells = water

Question 2

Why is water essential for life?

Answer 2

Water acts as:
A solvent
A reactant or products in reactants
An organizing principle

Question 3

Organizing Principle

Answer 3

Ability for a solute to dissolve in water; interactions of dissolving or not dissolving cannot mix

Question 4

Water’s Chemical Properties Contribute To Its Solvent Properties

Answer 4

Polarity & H-bonds

Reversible ionization

Question 5

Polarity

Answer 5

Determination: Arrangement of electrons in a covalent bond
Equal sharing, uniform charge distribution: non-polar
Unequal sharing, asymmetrical distribution: polar; molecule is polar because the bond involves an electronegative atom (O>N>S>C>P>H)
Polar covalent bonds: more reactive when more electronegative therefore easier to react in a reaction

Question 6

Importance of polarity

Answer 6

Explains hydrophobic and hydrophilic molecules; ability to interact with non-polar and polar aspects of different molecules
Water as an organizing principle
Leads to non-covalent interactions

Question 7

Types of noncovalent interactions

Answer 7

H bonds
Electrostatic, ionic interactions
Van der waals interactions
Hydrophobic interactions

Question 8

Hydrogen bonds

Answer 8

Occurs between electronegative atom (H bond acceptor) & an H atom that is covalently bonded to another atom (donor)
Water forms H bonds with other water molecules
Water forms extensive bonds with itself; forms lattice network; very short lived
Number of H bonds determine the shape or structure of water (gas, liquid, solid)
More H bonds means higher boiling pt and lower melting point
Temperature changes organization of water; makes bonds shorter lived; H bonds can be broken/disrupted by temp.; need constant body temp.

Question 9

H bonds

Answer 9

Weak associations: ~1-5 kcal/mol vs. 50-200 kcal/mol for covalent bond
Directionality
Rapidly form, break, reform in different orientation
Has partial charges

Question 10

Importance of H bonds

Answer 10

Solvent properties; structure of proteins and nucleic acids (DNA & RNA)
Small input of energy needed to break bond compared to covalent bonds (requires large input of energy or a catalyst)
Protein shape determines function & linear sequence determines shape; temperature in mammals is constant to prevent destruction of macromolecules
Every bond in DNA must be broken in order to copy each individual strand; if not H bond, then unable to function properly

Question 11

Electrostatic, ionic interactions

Answer 11

Attraction/repulsion of charges
Occurs between atoms with complete (-) charge & a complete (+) charge
Strength of interaction determined by distance and covalent

Question 12

Importance of Electrostatic Interactions

Answer 12

Protein-protein interactions, DNA-protein interactions, catalytic mechanisms

Question 13

Why are salts soluble in water?

Answer 13

NaCl dissociates in water due to partial charges

Question 14

Van de waals forces

Answer 14

Charge fluctuations: transiently produces +/- poles, even in nonpolar and hydrophobic molecules
Present with “snug fit” between atoms
Weakest noncovalent interactions (0.1-1 kcal/mol)

Question 15

Hydrophobic Interactions: Hydrophobic Effects

Answer 15

Involves nonpolar molecules
Nonpolar cannot form H bonds with water because nonpolar molecules do not have electronegative atoms– unable to form electrostatic interactions

Question 16

Favorability of hydrophobic interactions

Answer 16

Entropy (S)
Measure is disorder: ordered state= low energy; disordered state= high energy
Possible arrangements of molecules = any interactions that increase entropy = disorder

Question 17

Hydrophobic Effect

Answer 17

Entropy driven
Hydrophobic interactions form spontaneously
Importance to structure/function
Cell membranes form because of hydrophobic effect
Major determinant of protein folding

Question 18

Importance of Noncovalent Interactions

Answer 18

Weak and transient: gives flexibility to macromolecules
Provide stability to macromolecular structures - large numbers are present in molecule; unlikely that all will be broken at the same time
Essential to specificity and catalytic efficiency of enzymes (biological catalysts)