Chapter 3: The Molecules of Cells – Study Notes

Introduction to Organic Compounds

Overview

Organic compounds are the foundation of cellular structure and function. Their diversity arises from the unique properties of carbon, which forms the backbone of these molecules.

• Organic compounds are molecules containing carbon atoms bonded to other carbons and/or other elements.

• Carbon can form up to four covalent bonds, allowing for a variety of structures such as chains, branches, and rings.

• Methane (CH4) is a simple organic molecule, illustrating carbon's tetrahedral bonding.

3.1 Life’s Molecular Diversity Is Based on the Properties of Carbon

Hydrocarbons and Isomers

Hydrocarbons and isomers demonstrate the versatility of carbon in forming diverse molecular structures.

• Hydrocarbons: Molecules composed only of carbon and hydrogen. Their structure can vary in length, branching, and the presence of double bonds.

• Isomers: Compounds with the same molecular formula but different structures. Types include structural, geometric, and enantiomers, each with distinct functional properties.

Type	Example	Key Feature
Structural Isomer	Pentane vs. 2-methylbutane	Different connectivity
Geometric Isomer	Cis/trans 2-butene	Different spatial arrangement around double bond
Enantiomer	L- and D- forms	Mirror images

3.2 Chemical Groups Key to Biological Molecules

Functional Groups

Functional groups are specific clusters of atoms that confer distinct chemical properties to organic molecules.

• Hydroxyl group (-OH): Polar; found in alcohols.

• Carbonyl group (C=O): Polar; found in aldehydes and ketones.

• Carboxyl group (-COOH): Acidic; found in carboxylic acids.

• Amino group (-NH2): Basic; found in amines.

• Phosphate group (-PO4): Ionized; found in nucleic acids.

• Methyl group (-CH3): Nonpolar; affects gene expression.

Functional groups determine the reactivity and interactions of biological molecules. For example, testosterone and estradiol differ only in a few functional groups, resulting in distinct biological effects.

3.3 Cells Make Large Molecules from Small Molecules

Macromolecules and Polymers

Cells synthesize large molecules (macromolecules) by linking smaller units (monomers) into polymers.

• Macromolecules: Large biological molecules, including carbohydrates, proteins, nucleic acids, and some lipids.

• Polymers: Chains of monomers joined by covalent bonds.

• Dehydration synthesis: Reaction that joins monomers by removing water.

• Hydrolysis: Reaction that breaks polymers into monomers by adding water.

• Enzymes: Biological catalysts that regulate these reactions.

Equation for Dehydration Synthesis:

$\text{Monomer}_1 + \text{Monomer}_2 \xrightarrow{\text{Enzyme}} \text{Polymer} + H_2O$

Equation for Hydrolysis:

$\text{Polymer} + H_2O \xrightarrow{\text{Enzyme}} \text{Monomer}_1 + \text{Monomer}_2$

3.4 Carbohydrates

Monosaccharides

Carbohydrates are sugars and their polymers, serving as energy sources and structural materials.

• Monosaccharides: Simple sugars (e.g., glucose, fructose) with the formula (CH2O)n.

• Contain hydroxyl and carbonyl groups.

• Used as fuel for cellular work and as raw materials for building other molecules.

Monosaccharide	Structure
Glucose	Six-carbon ring
Fructose	Five-carbon ring

Disaccharides

Two monosaccharides can join via dehydration synthesis to form a disaccharide.

• Maltose: Glucose + Glucose

• Sucrose: Glucose + Fructose

$\text{Glucose} + \text{Fructose} \rightarrow \text{Sucrose} + H_2O$

Polysaccharides

Polysaccharides are long chains of sugar units, serving as energy storage or structural components.

• Starch: Storage in plants

• Glycogen: Storage in animals

• Cellulose: Structural in plant cell walls

• Chitin: Structural in exoskeletons and fungal cell walls

Polysaccharide	Function	Location
Starch	Energy storage	Plants
Glycogen	Energy storage	Animals
Cellulose	Structure	Plant cell walls
Chitin	Structure	Exoskeletons, fungi

3.8 Lipids

Types and Functions

Lipids are hydrophobic molecules with diverse structures and functions, including energy storage, membrane structure, and signaling.

• Fats (triglycerides): Glycerol + 3 fatty acids; store energy.

• Phospholipids: Glycerol + 2 fatty acids + phosphate group; form cell membranes.

• Steroids: Four fused rings; include cholesterol and hormones.

Fats store more energy per gram than carbohydrates ($1\text{g fat} = 9$ calories, $1\text{g carb} = 4$ calories).

Saturated vs. Unsaturated Fats

• Saturated fatty acids: No double bonds; solid at room temperature.

• Unsaturated fatty acids: One or more double bonds; liquid at room temperature due to kinks in the chain.

• Trans fats: Produced by hydrogenating unsaturated fats; associated with health risks.

3.10 Phospholipids and Steroids

Phospholipids

Phospholipids are essential for cell membrane structure, forming bilayers with hydrophilic heads and hydrophobic tails.

• Amphiphilic nature allows formation of membranes in aqueous environments.

Steroids

• Cholesterol: Maintains membrane fluidity; precursor for steroid hormones.

• Anabolic steroids: Synthetic variants of testosterone; misuse can cause serious health issues.

3.12 Proteins

Functions and Structure

Proteins are polymers of amino acids with diverse functions, including catalysis, transport, defense, signaling, and structure.

• Enzymes: Catalyze biochemical reactions.

• Transport proteins: Move substances across membranes.

• Defensive proteins: Antibodies.

• Signal proteins: Hormones.

• Receptor proteins: Receive signals.

• Structural proteins: Collagen, keratin.

Amino Acids and Peptide Bonds

• Proteins are made from 20 different amino acids.

• Amino acids have a central carbon, amino group, carboxyl group, hydrogen atom, and variable R group.

• Peptide bonds form via dehydration synthesis between amino and carboxyl groups.

$\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Protein Structure

• Primary structure: Sequence of amino acids.

• Secondary structure: Alpha helix or beta sheet, stabilized by hydrogen bonds.

• Tertiary structure: Overall 3D shape due to R group interactions.

• Quaternary structure: Association of multiple polypeptide chains.

Protein function depends on shape; denaturation (by heat, pH, or salt) disrupts function.

3.15 Nucleic Acids: DNA & RNA

Structure and Function

Nucleic acids are polymers of nucleotides, storing and transmitting genetic information.

• Nucleotide: Composed of a five-carbon sugar (ribose or deoxyribose), phosphate group, and nitrogenous base.

• DNA bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).

• RNA bases: Adenine (A), Uracil (U), Cytosine (C), Guanine (G).

• DNA is double-stranded (double helix); RNA is single-stranded.

• Genes (DNA segments) encode proteins via transcription (DNA to RNA) and translation (RNA to protein).

$\text{DNA} \xrightarrow{\text{Transcription}} \text{RNA} \xrightarrow{\text{Translation}} \text{Protein}$

Summary Table: Major Classes of Biological Molecules

Class	Monomer	Polymer	Main Functions
Carbohydrates	Monosaccharide	Polysaccharide	Energy, structure
Lipids	Fatty acid, glycerol	Triglyceride, phospholipid, steroid	Energy storage, membranes, signaling
Proteins	Amino acid	Polypeptide	Catalysis, structure, transport, defense
Nucleic Acids	Nucleotide	DNA, RNA	Genetic information