Carbon: The Framework of Biological Molecules

Importance of Carbon in Biological Molecules

Carbon is the central element in biological molecules due to its unique ability to form four covalent bonds, allowing for a diversity of stable and complex structures.

• Carbon atoms can bond to other carbon atoms, as well as to elements such as nitrogen (N), sulfur (S), phosphorus (P), oxygen (O), and hydrogen (H).

• Carbon forms the backbone of hydrocarbons, which are molecules consisting only of carbon and hydrogen. These are typically nonpolar and hydrophobic.

• The versatility of carbon enables the formation of chains, rings, and branched structures, which are foundational to the diversity of organic molecules.

Functional Groups

Functional groups are specific groups of atoms within molecules that have characteristic properties and chemical reactivity.

• They bond to the carbon-hydrogen core of organic molecules.

• Each functional group imparts unique chemical properties to the molecule.

• The properties of functional groups are retained wherever they attach, influencing the behavior and reactivity of the entire molecule in chemical reactions.

• Examples: Hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4), methyl (-CH3).

Isomers

Isomers are molecules with the same molecular or empirical formula but different structures or spatial arrangements.

• Structural isomers: Differ in the arrangement of their carbon skeleton.

• Stereoisomers: Differ in the spatial arrangement of atoms/groups attached to the carbon skeleton.

• Enantiomers: Mirror-image isomers, often referred to as chiral molecules. A chiral carbon has four different groups attached.

• Examples: D-sugars and L-amino acids are biologically relevant enantiomers.

Modern Biochemistry

Scope of Biochemistry

Modern biochemistry studies biological molecules outside of living cells, focusing on the structure, function, and interactions of biological macromolecules.

• Main classes of biological macromolecules:

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic Acids

Enzyme-Free Fermentation

Scientific Thinking: Fermentation Outside Living Cells

Fermentation is a chemical reaction, often catalyzed by enzymes, that can occur outside of living cells under certain conditions.

• When yeast cells are broken open, their enzymes can function outside the cell to catalyze fermentation.

• Experiments using ground yeast and fermentable substrates (e.g., glucose) demonstrate that CO2 is produced, indicating fermentation can occur without intact living cells.

• Nonfermentable substrates do not produce CO2.

• Significance: This allows the study of biochemical reactions in vitro and the purification of proteins/enzymes for research.

Macromolecules: Polymers and Monomers

Polymers and Monomers

Most biological macromolecules are polymers, large molecules made by linking together smaller subunits called monomers.

• Polymer: A large molecule made of repeating monomer units.

• Monomer: A small, similar chemical subunit.

• Examples:

  • Carbohydrates: Monomer = monosaccharide

  • Proteins: Monomer = amino acid

  • Nucleic acids: Monomer = nucleotide

Assembly and Disassembly of Polymers

• Dehydration synthesis (condensation reaction): Formation of large molecules by the removal of water. Monomers are joined to form polymers.

• Hydrolysis: Breakdown of large molecules by the addition of water. Polymers are broken down to monomers.

Carbohydrates: Energy Storage and Structural Molecules

Structure and Function

Carbohydrates are organic molecules with a 1:2:1 ratio of carbon, hydrogen, and oxygen (empirical formula: (CH2O)n).

• Serve as energy storage (e.g., glucose, starch, glycogen) and structural components (e.g., cellulose, chitin).

• Covalent bonds in carbohydrates store significant energy.

Types of Carbohydrates

• Monosaccharides: Simple sugars (e.g., glucose, fructose, galactose). Six-carbon sugars (hexoses) are especially important in biology.

• Disaccharides: Two monosaccharides linked by dehydration synthesis (e.g., sucrose, lactose, maltose). Used for sugar transport and energy storage.

• Polysaccharides: Long chains of monosaccharides linked by dehydration synthesis. Used for energy storage (starch in plants, glycogen in animals) and structural support (cellulose in plants, chitin in arthropods and fungi).

Isomerism in Sugars

• Glucose, fructose, and galactose are isomers with the same molecular formula but different structures.

• Enzymes can distinguish between structural and stereoisomers, affecting metabolism and function.

Nucleic Acids: Information Molecules

Structure and Function

Nucleic acids store and transmit genetic information. They are polymers of nucleotides.

• Nucleotide: Consists of a five-carbon sugar (deoxyribose in DNA, ribose in RNA), a phosphate group, and a nitrogenous base.

• Nitrogenous bases:

  • Purines: Adenine (A), Guanine (G)

  • Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA)

• Nucleotides are joined by phosphodiester bonds to form nucleic acid polymers.

DNA and RNA

• DNA (Deoxyribonucleic Acid): Double helix structure, stores genetic information, base pairing: A-T, G-C.

• RNA (Ribonucleic Acid): Single-stranded, contains uracil instead of thymine, involved in protein synthesis and gene expression.

Other Nucleotides

• ATP (Adenosine Triphosphate): Primary energy currency of the cell.

• NAD+ (Nicotinamide Adenine Dinucleotide) and FAD (Flavin Adenine Dinucleotide): Electron carriers in cellular respiration.

Proteins: Molecules with Diverse Structures and Functions

Functions of Proteins

Proteins are the most diverse macromolecules, performing a wide range of functions in the cell.

• Enzyme catalysis

• Defense (e.g., antibodies)

• Transport (e.g., hemoglobin)

• Support (e.g., collagen)

• Motion (e.g., actin, myosin)

• Regulation (e.g., hormones)

• Storage (e.g., casein)

Structure of Proteins

• Proteins are polymers of amino acids, linked by peptide bonds.

• Amino acid structure: Central carbon atom, amino group (NH2), carboxyl group (COOH), hydrogen atom, and variable R group (side chain).

• There are 20 common amino acids, each with a unique R group.

Levels of Protein Structure

• Primary structure: Sequence of amino acids.

• Secondary structure: Local folding patterns (α-helix, β-pleated sheet) stabilized by hydrogen bonds.

• Tertiary structure: Overall 3D shape of a single polypeptide, stabilized by various interactions (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions).

• Quaternary structure: Arrangement of multiple polypeptide subunits in a protein.

Protein Motifs and Domains

• Motifs: Common elements of secondary structure found in many proteins, useful for predicting function.

• Domains: Functional units within a protein, often associated with specific activities.

Protein Folding and Chaperones

• Proteins must fold into their correct 3D shape to function properly.

• Chaperone proteins assist in the folding process and prevent misfolding.

• Defects in chaperones can lead to diseases (e.g., cystic fibrosis).

Denaturation

• Denaturation is the loss of protein structure (and function) due to environmental changes (temperature, pH, ionic concentration).

• Denatured proteins may not refold correctly, leading to loss of biological activity.

Lipids: Hydrophobic Molecules

Characteristics and Diversity

Lipids are a diverse group of hydrophobic molecules, insoluble in water due to a high proportion of nonpolar C–H bonds.

• Include fats, oils, waxes, terpenes, steroids, and some vitamins.

Fats and Triglycerides

• Triglycerides: Composed of one glycerol and three fatty acids.

• Fatty acids may vary in chain length and saturation.

• Saturated fats: No double bonds, higher melting point, usually animal origin.

• Unsaturated fats: One or more double bonds, lower melting point, usually plant origin.

• Trans fats: Produced industrially, associated with health risks.

Phospholipids

• Composed of glycerol, two fatty acids (nonpolar tails), and a phosphate group (polar head).

• Major component of biological membranes.

• Form bilayers in aqueous environments, with hydrophilic heads facing outward and hydrophobic tails inward.

Steroids and Other Lipids

• Steroids: Lipids with a four-ring structure (e.g., cholesterol, hormones).

• Terpenes: Long-chain lipids, components of pigments and vitamins.

Table: Comparison of Biological Macromolecules