Chapter 2: The Chemistry of the Cell – Study Notes

The Chemistry of the Cell

Introduction

This chapter explores the foundational chemical principles that underlie cell structure and function. Five key principles are emphasized: the characteristics of carbon, the characteristics of water, selectively permeable membranes, synthesis by polymerization of small molecules, and self-assembly.

2.1 The Importance of Carbon

Organic and Biological Chemistry

• Organic chemistry is the study of carbon-containing compounds.

• Biological chemistry (biochemistry) focuses on the chemistry of living systems, where carbon is the central atom in most biological molecules.

Bonding Properties of the Carbon Atom

• Carbon has a valence of 4, allowing it to form four covalent bonds with other atoms.

• Common bonding partners include oxygen (O), hydrogen (H), nitrogen (N), and sulfur (S).

• Covalent bonds involve the sharing of electron pairs between atoms.

Biologically Important Atoms and Their Valences

Atom	Valence
Carbon (C)	4
Hydrogen (H)	1
Oxygen (O)	2
Nitrogen (N)	3

Covalent Bonding of Carbon Atoms

• Single bonds: sharing one pair of electrons.

• Double bonds: sharing two pairs of electrons.

• Triple bonds: sharing three pairs of electrons.

• Regardless of bond type, carbon forms four covalent bonds.

Examples of Simple Organic Molecules

Molecule	Formula	Bond Type
Methane	CH4	Single
Ethanol	CH3CH2OH	Single
Methylamine	CH3NH2	Single
Ethylene	CH2=CH2	Double
Carbon dioxide	CO2	Double
Molecular nitrogen	N2	Triple
Hydrogen cyanide	HCN	Triple
Acetylene	CH≡CH	Triple

Stability of Carbon-Containing Molecules

• Bond energy is the energy required to break 1 mole of bonds, measured in calories per mole (cal/mol).

• 1 kcal (kilocalorie) = 1000 calories.

Bond Energies of Covalent Bonds

Bond	Bond Energy (kcal/mol)
C—C	83
C—N	70
C—O	84
C—H	99
C=C	146
C≡C	212

Strong Covalent Bonds and Life

• Solar radiation's energy is inversely related to wavelength.

• Visible light cannot break C—C bonds, making organic molecules stable under sunlight.

• Ultraviolet light, with higher energy, can be hazardous to biological molecules.

Diversity of Carbon-Containing Molecules

• Carbon forms a wide variety of compounds due to its bonding versatility.

• Carbon chains can be linear, branched, or form rings, with single or double bonds.

Hydrocarbons

• Hydrocarbons are chains or rings of only carbon and hydrogen.

• They are important in industry (e.g., fuels) but are not water-soluble, limiting their biological roles except in membranes.

Biological Compounds and Functional Groups

• Biological molecules often contain O, N, P, or S, usually as part of functional groups that confer specific chemical properties.

Functional Group	Charge/Polarity
Carboxyl, Phosphate	Negatively charged
Amino	Positively charged
Hydroxyl, Sulfhydroxyl, Carbonyl, Aldehyde	Uncharged but polar

Bond Polarity

• Polar bonds result from unequal sharing of electrons, often due to high electronegativity (e.g., O, S).

• Polar bonds increase water solubility compared to nonpolar C—C or C—H bonds.

Stereoisomers and Asymmetric Carbon Atoms

• Carbon's tetrahedral geometry allows for stereoisomers—nonsuperimposable mirror images.

• An asymmetric carbon atom has four different substituents, leading to two stereoisomers per asymmetric carbon.

• A molecule with n asymmetric carbons has $2^n$ possible stereoisomers.

2.2 The Importance of Water

Role of Water in Cells

• Water is the universal solvent and the most abundant component of cells (75–85% by weight).

• Essential for life and cellular processes.

Transport of Water

• Water moves in and out of cells and between cells.

• Osmosis: movement of water across membranes based on solute concentration.

• Aquaporins (AQP): channel proteins that facilitate rapid water movement.

Polarity of Water

• Water's polarity is responsible for its cohesiveness, temperature-stabilizing capacity, and solvent properties.

Water Molecules Are Polar

• Water has a bent shape; oxygen is highly electronegative, creating partial negative (O) and positive (H) charges.

Cohesiveness and Hydrogen Bonds

• Water molecules are attracted to each other via hydrogen bonds (about 1/10 the strength of covalent bonds).

• This network gives water high surface tension, boiling point, specific heat, and heat of vaporization.

Surface Tension of Water

• Surface tension results from hydrogen bonds, allowing insects to walk on water and water to move in plants.

Temperature-Stabilizing Capacity

• Water's high specific heat (1.0 cal/g/°C) allows it to absorb heat without large temperature changes, protecting cells from thermal fluctuations.

Heat of Vaporization

• High energy is required to vaporize water, making it an effective coolant.

Water as a Solvent

• Water dissolves many substances due to its polarity, forming hydrogen or ionic bonds with solutes.

Solutes: Hydrophilic and Hydrophobic

• Hydrophilic solutes dissolve easily in water (e.g., sugars, organic acids, some amino acids).

• Hydrophobic molecules (e.g., lipids, membrane proteins) do not dissolve in water.

NaCl in Water

• NaCl dissociates into Na+ and Cl− ions in water.

• Water molecules form spheres of hydration around ions, reducing their tendency to reassociate.

Solubility of Molecules with No Net Charge

• Some uncharged molecules are still hydrophilic due to localized charges.

• Hydrophobic molecules disrupt water's hydrogen bonding and are repelled.