Chapter 2 – Chemical Foundations
2.1 Covalent Bonds and Noncovalent Interactions
2.2 Chemical Building Blocks of Cells
2.3 Chemical Reactions and Chemical Equilibrium
2.4 Biochemical Energetics
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Chapter 2 – Chemical Foundations
• 2.1 Covalent Bonds and Noncovalent Interactions
– Molecules: hydrophilic, hydrophobic, and amphipathic
– Covalent bonds: shared electron pairs arrange specific
molecular geometries such as stereoisomers around asymmetric
carbons; unequal electron sharing yields polar covalent bonds
with partial charges; more stable than weaker noncovalent
interactions
– Four types of biological noncovalent interactions: ionic bonds
(electrostatic interactions), hydrogen bonds (nonbonding
electron hydrogen attraction), van der Waals interactions
(transient dipole interactions) , and hydrophobic effect
interactions (reduces contact with water)
– Molecular complementarity: fit between molecular shapes,
charges, and other physical properties
Simulation of ice formation
2.1 Covalent Bonds and Noncovalent Interactions
2.2 Chemical Building Blocks of Cells
2.3 Chemical Reactions and Chemical Equilibrium
2.4 Biochemical Energetics
– Macromolecule polymers of monomer subunits: proteins-amino
acids; nucleic acids-nucleotides; polysaccharides-
monosaccharides
– Proteins: differences in size, shape, charge, hydrophobicity, and
reactivity of the 20 common amino acid side chains determine
protein chemical and structural properties
– Nucleic acids: purine A and G, and pyrimidine C, T (DNA), and U
(RNA) nucleotide bases comprise DNA and RNA
– Polysaccharides: hexoses (glucose and others) linked by two
types of bonds
– Membranes: amphipathic phospholipids with saturated or
unsaturated tails associate noncovalently to form bilayer
membrane structure
Clicker Question 2-1
Which of the following represent covalent interactions?
A. peptide bond formation during the translation of epidermal growth
factor (EGF)
B. disulfide formation during folding of the newly translated EGF
C. ionic bond formation during folding of the newly translated EGF
D. hydrogen bond formation during folding of the newly translated
EGF
E. Both A and B
Clicker Question 2-1
Which of the following represent covalent interactions?
A. peptide bond formation during the translation of epidermal growth
factor (EGF)
B. disulfide formation during folding of the newly translated EGF
C. ionic bond formation during folding of the newly translated EGF
D. hydrogen bond formation during folding of the newly translated
EGF
E. Both A and B
Clicker Question 2-2
Which of the following accurately describe the molecule shown below?
CH3(CH2)7CH=CH(CH2)7COOH
A. hydrophilic
B. hydrophobic
C. polyunsaturated
D. saturated
E. None of the above
Clicker Question 2-2
Which of the following accurately describes the molecule shown below?
A. hydrophilic
B. hydrophobic
C. polyunsaturated
D. saturated
E. None of the above
CH3(CH2)7CH=CH(CH2)7COOH
Because of the single double carbon bond,
oleate is a monounsaturated fatty acid.
Clicker Question 2-3
Which of the following cell monomers do NOT form
structures using covalent bonds?
A) Amino acids
B) Nucleotides
C) Phospholipids
D) Monosaccharides
E) Actually, these all polymerize using covalent bonds.
Clicker Question 2-3
Which of the following cell monomers do NOT form structures
using covalent bonds?
A) Amino acids Amino acids are linked by peptide bonds.
B) Nucleotides
C) Phospholipids
D) Monosaccharides
E) Actually, these all polymerize using covalent bonds.
2.1 Covalent Bonds and Noncovalent Interactions
2.2 Chemical Building Blocks of Cells
2.3 Chemical Reactions and Chemical Equilibrium
2.4 Biochemical Energetics
– Chemical reactions: Keq=product/reactant ratio when forward
and reverse rates are equal
– Cell linked reactions are at steady state not equilibrium
– Dissociation constant(Kd) is measure of noncovalent interactions
– pH (-log[H+]): cytoplasm (pH 7.2-7.4) but lower in some
organelles (lysosome, pH 4.5)
– Acids release protons (H+); base bind protons
– Biological system uses weak acid/base buffers to maintain pH in
narrow ranges.
2.1 Covalent Bonds and Noncovalent Interactions
2.2 Chemical Building Blocks of Cells
2.3 Chemical Reactions and Chemical Equilibrium
2.4 Biochemical Energetics
– G: measure of reaction change in free energy; -G reactions are
thermodynamically favorable; +G reactions are not
– free energy change G0’ (-2.3 RTlog Keq): calculated from
reactants/products at equilibrium
– rate of reaction: depends on activation energy; lowered by a
catalyst
– −G reaction such as ATP hydrolysis to ADP + Pi can drive
coupled +G reaction.
– sun light energy captured by photosynthesis is ultimate source of
all cell energy
– coenzyme (NAD+, FAD) oxidation (loss of e-) and reduction (gain
of e-) electron transfer stores and transfers cell energy