Biomolecules: Carbohydrates, Proteins, and Nucleic Acids – Structure and Function

Biomolecules: Structure and Function

Key Terms and Definitions

• Carbon skeleton: The chain of carbon atoms that forms the foundation of organic molecules.

• Hydrocarbon: Molecules consisting entirely of carbon and hydrogen; nonpolar and hydrophobic.

• Functional group: Specific groups of atoms attached to carbon skeletons that confer chemical properties (e.g., hydroxyl, amino, carboxyl).

• Hydroxyl group (-OH): A functional group that makes molecules polar and hydrophilic.

• Amino group (-NH2): A functional group found in amino acids; acts as a base.

• Carboxyl group (-COOH): A functional group found in amino acids and fatty acids; acts as an acid.

• Monomer: A small molecule that can join with others to form polymers.

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

• Dehydration synthesis: A chemical reaction that joins monomers by removing water.

• Hydrolysis: A chemical reaction that breaks polymers into monomers by adding water.

• Carbohydrate: Organic molecules composed of carbon, hydrogen, and oxygen; includes sugars and starches.

• Monosaccharide: Simple sugar; monomer of carbohydrates (e.g., glucose).

• Disaccharide: Two monosaccharides joined together (e.g., sucrose).

• Polysaccharide: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

• Starch: Storage polysaccharide in plants.

• Glycogen: Storage polysaccharide in animals.

• Cellulose: Structural polysaccharide in plant cell walls.

• Amino acid: Monomer of proteins; contains amino and carboxyl groups.

• Protein: Polymer of amino acids; performs diverse functions in cells.

• Peptide: Short chain of amino acids.

• Polypeptide: Long chain of amino acids; folds into a protein.

• R-group: Side chain of an amino acid; determines its properties.

• Peptide bond: Covalent bond joining amino acids in a polypeptide.

• N-terminus: The end of a polypeptide with a free amino group.

• C-terminus: The end of a polypeptide with a free carboxyl group.

• α-helix: A common secondary structure in proteins; spiral shape stabilized by hydrogen bonds.

• β-sheet: Another secondary structure; sheet-like arrangement stabilized by hydrogen bonds.

• Primary structure: Sequence of amino acids in a protein.

• Secondary structure: Local folding patterns (α-helix, β-sheet) due to hydrogen bonding.

• Tertiary structure: Overall 3D shape of a protein due to interactions among R-groups.

• Quaternary structure: Association of multiple polypeptide chains.

• Enzyme: Protein that catalyzes biochemical reactions.

• Substrate: The molecule upon which an enzyme acts.

• Active site: Region of an enzyme where substrate binds and reaction occurs.

• DNA: Deoxyribonucleic acid; stores genetic information.

• RNA: Ribonucleic acid; involved in protein synthesis.

• Nucleic acid: Polymer of nucleotides; includes DNA and RNA.

• Ribose sugar: Five-carbon sugar in RNA.

• Phosphate group: Functional group in nucleotides; links nucleotides together.

• Polar: Molecules with uneven charge distribution; hydrophilic.

• Hydrophilic: Water-loving; dissolves in water.

• Nucleotide: Monomer of nucleic acids; consists of a sugar, phosphate, and nitrogenous base.

• Nitrogenous base: Component of nucleotides; includes adenine, guanine, cytosine, thymine, uracil.

• Antiparallel: Two strands of DNA run in opposite directions.

• Complementary: Bases pair specifically (A-T, G-C in DNA).

• Double-stranded: DNA consists of two strands.

• Single-stranded: RNA consists of one strand.

• 5’ end: End of nucleic acid with a free phosphate group.

• 3’ end: End of nucleic acid with a free hydroxyl group.

• Purines: Double-ring nitrogenous bases (adenine, guanine).

• Pyrimidines: Single-ring nitrogenous bases (cytosine, thymine, uracil).

Properties of Carbon in Biomolecules

Why Carbon Is a Good Backbone

Carbon is uniquely suited to form the backbone of large biological molecules due to its versatile bonding properties.

• Four valence electrons: Allows carbon to form four covalent bonds, enabling complex structures.

• Ability to form chains and rings: Carbon atoms can link together in long chains or rings, creating diverse skeletons.

• Stable bonds: Carbon-carbon bonds are stable, allowing for large, durable molecules.

• Bonding with many elements: Carbon can bond with hydrogen, oxygen, nitrogen, phosphorus, and sulfur, forming a variety of functional groups.

• Isomerism: Carbon compounds can exist as structural, geometric, or optical isomers, increasing diversity.

Polymer Formation and Breakdown

Dehydration Synthesis and Hydrolysis

Biological polymers are assembled and disassembled through two key chemical reactions.

• Dehydration synthesis: Joins monomers by removing a molecule of water. Used to build polymers such as proteins, carbohydrates, and nucleic acids.

• Hydrolysis: Breaks polymers into monomers by adding water. Used in digestion and recycling of biomolecules.

Example: Formation of a peptide bond between two amino acids via dehydration synthesis.

Equation:

$\text{Amino acid}_1 + \text{Amino acid}_2 \xrightarrow{\text{dehydration}} \text{Dipeptide} + \text{H}_2\text{O}$

Additional info: These reactions are catalyzed by enzymes in cells.

Major Categories of Biomolecules

Carbohydrates

Carbohydrates are energy sources and structural molecules in cells.

• Building blocks: Monosaccharides (e.g., glucose, fructose).

• Structural features: Carbon skeleton with multiple hydroxyl groups; often forms rings in solution.

• Chemical properties: Polar, hydrophilic; can form glycosidic bonds.

• Examples: Starch (plant storage), glycogen (animal storage), cellulose (plant structure).

Proteins

Proteins perform a wide range of functions, including catalysis, structure, and signaling.

• Building blocks: Amino acids (20 types).

• Structural features: Central carbon with amino, carboxyl, hydrogen, and R-group.

• Chemical properties: Vary depending on R-group; can be polar, nonpolar, acidic, or basic.

• Examples: Enzymes, structural proteins (collagen), transport proteins (hemoglobin).

Nucleic Acids

Nucleic acids store and transmit genetic information.

• Building blocks: Nucleotides (sugar, phosphate, nitrogenous base).

• Structural features: Sugar-phosphate backbone; nitrogenous bases project inward.

• Chemical properties: Polar, hydrophilic backbone; bases can form hydrogen bonds.

• Examples: DNA (double-stranded), RNA (single-stranded).

Protein Structure and Folding

From Polypeptide to Protein

A linear polypeptide folds into a functional three-dimensional protein through several structural levels.

• Primary structure: Sequence of amino acids.

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

• Tertiary structure: Overall 3D shape due to interactions among R-groups (hydrophobic, ionic, hydrogen bonds, disulfide bridges).

• Quaternary structure: Association of multiple polypeptide chains.

Example: Hemoglobin has quaternary structure with four polypeptide subunits.

Chemical Reactions and Protein Structure Levels

Chemical Reaction	Protein Structure Level
Hydrogen bonding between carboxyl (C=O) and amino (N-H) groups	Secondary structure
Interaction of multiple, independent units (polypeptides)	Quaternary structure
Order of amino acids linked together in a chain	Primary structure
Interaction of R-groups of each amino acid	Tertiary structure

Importance of Protein Shape

The three-dimensional shape of a protein determines its function. Misfolded proteins can lose function or cause disease (e.g., sickle cell anemia).

• Enzyme specificity: Shape of active site allows binding to specific substrates.

• Structural proteins: Shape provides mechanical support (e.g., collagen).

Protein vs. Nucleic Acid Diversity

Proteins can form more diverse shapes than nucleic acids due to the variety of R-groups in amino acids, which allow for many types of interactions. Nucleic acids have a more uniform backbone and limited base pairing.

• Proteins: 20 amino acids with diverse R-groups.

• Nucleic acids: 4 bases; backbone is chemically similar throughout.

Additional info: This diversity enables proteins to serve as enzymes, structural components, and signaling molecules.

Nucleic Acid Structure

Backbone Construction

The backbone of nucleic acid polymers is formed by joining the phosphate group of one nucleotide to the 3’ hydroxyl group of another via dehydration synthesis.

• Functional groups joined: Phosphate and hydroxyl.

• Chemical process: Dehydration synthesis.

Equation:

$\text{Nucleotide}_1 + \text{Nucleotide}_2 \xrightarrow{\text{dehydration}} \text{Dinucleotide} + \text{H}_2\text{O}$

Hydrogen Bonding in Nucleotides

Nucleotides readily form hydrogen bonds due to the presence of polar groups in their nitrogenous bases. These bonds are essential for base pairing in DNA and RNA.

• Base pairing: Adenine pairs with thymine (or uracil in RNA), guanine pairs with cytosine.

• Hydrogen bond donors and acceptors: Nitrogen and oxygen atoms in bases provide sites for hydrogen bonding.

Example: In DNA, A-T pairs form two hydrogen bonds; G-C pairs form three hydrogen bonds.

Additional info: Hydrogen bonds stabilize the double helix structure of DNA.