Chemical Components of Cells: Structure, Function, and Biological Importance

Chemical Components of Cells

Overview

This chapter explores the fundamental chemical components of cells, focusing on the types of atoms, chemical bonds, and the properties of water that are essential for life. It also covers the calculation of pH, concentrations, and the structure/function relationships in biological macromolecules.

Atoms and Elements in Cells

Major Elements in Biological Systems

Cells are composed of a limited set of elements, with a few dominating biological chemistry. These elements are critical for cellular structure and function.

• Key Elements: Oxygen, Carbon, Hydrogen, Nitrogen, Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, Magnesium.

• Trace Elements: Boron, Chromium, Cobalt, Copper, Fluorine, Iodine, Iron, Manganese, Molybdenum, Selenium, Silicon, Vanadium, Zinc.

• Atomic Structure: Atoms consist of protons (positive charge), neutrons (neutral), and electrons (negative charge).

• Atomic Number: Number of protons; determines the element.

• Atomic Weight: Sum of protons and neutrons.

Chemical Bonds

Types of Chemical Bonds

Chemical bonds are the forces that hold atoms together in molecules. The nature of these bonds determines the stability and function of biological molecules.

• Covalent Bonds: Sharing of electrons between atoms; strongest type of bond in biological systems.

• Ionic Bonds: Transfer of electrons from one atom to another, resulting in charged ions.

• Hydrogen Bonds: Weak electrostatic attraction between a hydrogen atom in a polar bond and another electronegative atom.

• Hydrophobic Interactions: Nonpolar molecules aggregate to avoid water.

• Van der Waals Attractions: Weak, transient interactions due to temporary dipoles.

Bond Strengths and Properties

The strength of chemical bonds varies depending on the environment (vacuum vs water) and the type of bond.

• Covalent bonds: ~90 kcal/mol in vacuum and water.

• Ionic bonds: Strong in vacuum (~80 kcal/mol), much weaker in water (~3 kcal/mol).

• Hydrogen bonds: ~4 kcal/mol in vacuum, ~1 kcal/mol in water.

• Van der Waals: Very weak (~0.1 kcal/mol).

Properties of Water

Unique Properties of Water

Water is essential for life due to its polar nature and ability to form hydrogen bonds, which give rise to several unique properties.

• High specific heat and boiling point

• Liquid at room temperature

• Lower density as solid (ice floats)

• Surface tension, adhesion, and cohesion

Hydration and Solubility

Water's polarity allows it to dissolve ionic and polar substances by forming hydration shells around ions and molecules.

• Sphere of Hydration: Water molecules surround ions, partially shielding their charges.

• Ionic substances: Dissolve due to attraction between water and ions.

• Polar substances: Dissolve by forming hydrogen bonds with water.

Weak Interactions: Van der Waals and Hydrophobic Forces

Van der Waals Attractions

Van der Waals forces are weak interactions caused by transient electrical charges. They are significant when many such interactions occur between macromolecular surfaces.

• Transient dipoles: Cause attraction between atoms.

• Importance: Stabilize protein and nucleic acid structures.

Hydrophobic Interactions

Hydrophobic interactions occur when nonpolar molecules aggregate to minimize their exposure to water, driven by water's tendency to exclude nonpolar substances.

• Hydrophobic molecules: Insoluble in water; often hydrocarbons.

• Hydrophobic forces: Cause nonpolar groups to cluster together.

Solutions, Concentrations, and pH

The Mole and Molarity

Concentration is a critical concept in cell chemistry. The mole is a standard unit for quantifying atoms and molecules.

• Avogadro's number: $6 \times 10^{23}$ particles per mole.

• Molarity (M): Moles per liter of solution.

• Example: 1 M NaCl solution requires 58 g NaCl per liter.

pH and Ionization of Water

pH measures the concentration of hydrogen ions in solution, which is crucial for biological processes.

• Ionization of water: $\mathrm{H_2O \rightleftharpoons H^+ + OH^-}$

• Equilibrium constant: $K_w = [H^+][OH^-] = 1 \times 10^{-14}$

• pH formula: $\mathrm{pH = -log_{10}[H^+]}$

• Pure water: $[H^+] = 1 \times 10^{-7}$, pH = 7

• Acids: Donate protons (H+)

• Bases: Accept protons (H+)

• Buffers: Resist changes in pH; consist of weak acid/base and their conjugate forms.

Functional Groups in Biological Molecules

Common Functional Groups

Functional groups are specific groups of atoms within molecules that confer characteristic chemical properties.

• Methyl (-CH3): Nonpolar hydrocarbon

• Hydroxyl (-OH): Alcohols

• Carboxyl (-COOH): Weak acid

• Carbonyl (C=O): Ketones and aldehydes

• Amino (-NH2): Weak base

• Amide (O=C-NH2): Carboxyl + amine

• Phosphate (-PO3): Esters and anhydrides

• Sulfhydryl (-SH): Forms disulfide bonds

Biological Macromolecules

Carbon and Organic Chemistry

Carbon is the backbone of organic molecules due to its valency of four, allowing for diverse structures and isomerism.

• Hydrocarbons: Chains and rings of carbon and hydrogen.

• Isomers: Structural, geometric, and optical variations.

Major Classes of Biological Molecules

Cells contain four major classes of macromolecules: carbohydrates, lipids, nucleic acids, and proteins.

• Carbohydrates: Sugars and polysaccharides; energy storage and structural roles.

• Lipids: Fatty acids, triacylglycerols, phospholipids, cholesterol; energy storage, membrane structure, signaling.

• Nucleic Acids: DNA and RNA; information storage and transmission.

• Proteins: Polymers of amino acids; enzymatic, structural, signaling functions.

Condensation and Hydrolysis Reactions

Macromolecules are assembled by condensation reactions (removal of water) and broken down by hydrolysis (addition of water).

• Condensation: Formation of bonds between monomers, releasing water.

• Hydrolysis: Breaking bonds by adding water.

Carbohydrates: Structure and Function

Monosaccharides and Polysaccharides

Carbohydrates are composed of monosaccharides (simple sugars) and polysaccharides (complex carbohydrates).

• General formula: (CH2O)n

• Glucose: Most important hexose; exists in two ring forms.

• Polysaccharides: Energy storage (starch, glycogen) and structural (cellulose).

• Glycosidic bonds: Link monosaccharides in polysaccharides.

Lipids: Structure and Function

Fatty Acids and Triacylglycerols

Lipids are hydrophobic molecules used for energy storage and membrane structure.

• Fatty acids: Long hydrocarbon chains with a carboxyl group.

• Triacylglycerols: Fatty acids linked to glycerol by ester bonds.

• Phospholipids: Glycerol, two fatty acids, and a phosphate group; major membrane component.

• Cholesterol: Four-ring structure; membrane fluidity and precursor to steroid hormones.

Nucleic Acids: Structure and Function

Nucleotides and Nucleic Acid Assembly

Nucleic acids are polymers of nucleotides, essential for genetic information storage and transmission.

• Nucleotide: Base + pentose sugar + phosphate.

• Phosphodiester linkage: Joins nucleotides in DNA/RNA.

• Structural polarity: 5' phosphate and 3' hydroxyl ends.

• Complementary base pairing: A-T/U (2 H bonds), G-C (3 H bonds).

• DNA vs RNA: DNA is double-stranded, RNA is mostly single-stranded.

Proteins: Structure and Function

Amino Acids and Protein Assembly

Proteins are polymers of amino acids, each with unique side chains (R-groups) that determine their properties and functions.

• 20 common amino acids: Classified as nonpolar, acidic, basic, or uncharged polar.

• Peptide bonds: Amide linkage formed by condensation.

• Structural polarity: N-terminus (amino) and C-terminus (carboxyl).

• Sequence defines structure and function: Vast diversity due to different combinations.

Summary Table: Bond Types and Strengths

BOND TYPE	LENGTH (nm)	STRENGTH IN VACUUM (kcal/mol)	STRENGTH IN WATER (kcal/mol)
Covalent	0.15	90 (377)	90 (377)
Ionic (noncovalent)	0.25	80 (335)	3 (12.6)
Hydrogen bond	0.30	4 (16.7)	1 (4.2)
Van der Waals	0.35	0.1 (0.4)	0.1 (0.4)

Key Equations

• pH calculation: $\mathrm{pH = -log_{10}[H^+]}$

• Water ionization: $\mathrm{H_2O \rightleftharpoons H^+ + OH^-}$

• Equilibrium constant: $K_w = [H^+][OH^-] = 1 \times 10^{-14}$

Conclusion

Understanding the chemical components of cells, including the types of atoms, chemical bonds, and properties of water, is fundamental to microbiology. These principles underpin the structure and function of biological macromolecules and the processes essential for life.