Biological Macromolecules: Monomers, Polymers, and Their Functions

Monomers & Covalent Bonds

Polymers & Monomers

  • Biological Macromolecules: The term often used to describe biological polymers.

  • Polymer: A large number of monomers joined together.

  • Monomer: The individual repeating unit that makes up a polymer.

  • Many metabolic processes involve both the breaking and making of biological macromolecules.

Examples of Monomer-Polymer Relationships

  • Monosaccharide (e.g., glucose) \implies Starch, glycogen, cellulose

  • Amino acids \implies Polypeptides and proteins

  • Nucleotides \implies Nucleic acids

Dehydration Synthesis (Condensation Reaction)

  • Process: Two molecules of monomer join together with a covalent bond.

    • A molecule of water (\text{H}_2 ext{O}) is removed as a byproduct (hence 'dehydration').

    • One large molecule is produced (synthesized).

  • Polymer Formation: When this process happens repeatedly, a polymer forms, with a water molecule produced each time a new monomer joins.

  • This is a common theme in the building of many different types of biological macromolecules.

Hydrolysis

  • Meaning: 'lyze' (to break) and 'hydro' (with water).

  • Process: Covalent bonds in polymers are broken when water is added.

Nucleic Acids

Comparing DNA & RNA

Similarities

  • Both DNA and RNA are polynucleotides, meaning they are made up of many nucleotides linked together in a chain.

  • Each nucleotide unit in both DNA & RNA has three components:

    • A pentose sugar (deoxyribose in DNA, ribose in RNA).

    • A phosphate group.

    • A nitrogenous base.

  • These three components form nucleotide units that are connected by covalent bonds.

  • Once bonded, the nucleotide units form a linear molecule with discrete 5' and 3' ends.

  • The nitrogenous bases are oriented perpendicular to the sugar-phosphate backbone.

Differences

Property

DNA

RNA

Pentose sugar

Deoxyribose

Ribose

Bases

Adenine (A), Thymine (T), Cytosine (C), Guanine (G)

Adenine (A), Uracil (U), Cytosine (C), Guanine (G)

Number of strands

Double-stranded (double helix)

Single-stranded

Length

Very long polynucleotide chains

Relatively short chains compared to DNA

  • Key Distinction: RNA nucleotides contain Uracil (U) instead of Thymine (T), which is unique to DNA.

  • Examiner Tip: DNA or RNA are correctly described as polymers of nucleotides, not polymers of bases.

Proteins

Structure & Function in Proteins

  • Composition: Proteins are made of linear chains of monomers called amino acids.

  • Covalent Bonds: Amino acids are connected by covalent bonds called peptide bonds.

  • Determinants of Function: The sequence, type, and number of amino acids within a protein determine its unique 3 ext{D} shape and, consequently, its function.

  • Importance: Proteins are extremely important in cells as they form or function as:

    • Enzymes: Catalyze biochemical reactions.

    • Cell membrane proteins: e.g., carriers for transport.

    • Hormones: Chemical messengers.

    • Immunoproteins: e.g., immunoglobulins (antibodies).

    • Transport proteins: e.g., hemoglobin for oxygen transport.

    • Structural proteins: e.g., keratin (hair, nails) and collagen (connective tissue).

    • Contractile proteins: e.g., myosin (muscle contraction).

  • All expressed genes code for specific proteins, meaning all reactions necessary for life rely on protein function.

Amino Acid Structure

  • Monomers: Amino acids are the monomers of polypeptides.

  • Number: There are 20 common amino acids found in polypeptides in all living organisms.

  • Primary Structure Importance: The specific order of amino acids within a polypeptide (its primary structure) ultimately determines the overall shape of the protein.

  • General Structure: A central carbon atom (alpha-carbon) is bonded to four groups:

    • An amino terminus (- ext{NH}_2).

    • A carboxylic acid terminus (- ext{COOH}).

    • A hydrogen atom (- ext{H}).

    • An R group (side chain), which is unique for each amino acid.

  • R Group Properties: The chemical properties of the R group (hydrophobic, hydrophilic, or ionic) dictate interactions that determine the structure and function of that region of the protein.

Peptide Bonds

  • Formation: Amino acids connect by forming peptide bonds at the carboxyl terminus of the growing peptide chain through a dehydration synthesis reaction.

    • A hydroxyl group (- ext{OH}) is lost from the carboxylic group (- ext{COOH}) of one amino acid.

    • A hydrogen atom (- ext{H}) is lost from the amino group (- ext{NH}_2) of the neighboring amino acid.

    • The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid.

    • A molecule of water is released.

  • Dipeptides: Formed by the dehydration synthesis of two amino acids.

  • Polypeptides: Formed by the dehydration synthesis of many (three or more) amino acids.

  • Hydrolysis: During hydrolysis reactions, the addition of water breaks the peptide bonds, breaking polypeptides down into individual amino acids.

  • Examiner Tip: When asked to identify the peptide bond, look for where nitrogen is bonded to a carbon that has a double bond with an oxygen atom (- ext{C=O}- ext{NH}-). The R group is not involved in peptide bond formation.

Categories of Amino Acids by R Group

  • The R groups of the 20 amino acids fall into three main categories based on their side chain properties:

    • Hydrophobic (nonpolar side chains).

    • Hydrophilic (polar side chains).

    • Some hydrophilic amino acids are acidic or basic, based on the ionization of their side chain groups (- ext{COOH} or - ext{NH}_2) which are distinct from the primary amino and carboxyl groups attached to the central carbon atom.

  • Examiner Tip: You are not expected to memorize the R groups, but you should be able to recognize from a molecular diagram whether an amino acid is hydrophobic, hydrophilic, acidic, or basic.

Protein Structure (Four Levels)

  • These four levels of structure determine the function of a protein.

  • Polypeptide or protein molecules can range from three amino acids (e.g., Glutathione) to more than 34,000 amino acids (e.g., Titan).

1. Primary Structure

  • Definition: The unique sequence and order of amino acids in a polypeptide chain.

  • Determination: Determined by DNA within a cell, which instructs the cell to add specific amino acids in certain quantities and in a particular sequence.

  • Significance: This sequence directly affects the protein's shape and, therefore, its function. It is highly specific for each protein; even one alteration in the amino acid sequence can significantly affect protein function.

2. Secondary Structure

  • Definition: Arises from the folding of the amino acid chain into specific, repeating shapes.

  • Held Together by: Hydrogen bonds that form between the oxygen of the carboxyl group (- ext{C=O}) of one amino acid and the hydrogen of the amino group (- ext{NH}-) of another amino acid.

    • The hydrogen of - ext{NH} has an overall positive charge, while the oxygen of - ext{C=O} has an overall negative charge, facilitating hydrogen bond formation.

  • Common Shapes: Two main shapes can form due to these hydrogen bonds:

    • \alpha-helix (alpha-helix): Occurs when hydrogen bonds form between every fourth peptide bond, creating a coiled structure.

    • \beta-pleated sheet (beta-pleated sheet): Forms when the protein folds so that two parts of the polypeptide chain are parallel to each other, allowing hydrogen bonds to form between the folded layers.

  • Stability: Hydrogen bonds are relatively weak and can be easily broken by high temperatures and pH changes.

3. Tertiary Structure

  • Definition: The overall three-dimensional shape of a single polypeptide chain.

  • Held Together by: Additional bonds and interactions formed between the R groups (side chains) of the amino acids within the polypeptide.

    • Hydrogen bonds: Between polar R groups.

    • Disulphide bonds: Strong covalent bonds formed between two cysteine amino acids (containing sulfur).

    • Ionic bonds: Between oppositely charged (acidic and basic) R groups.

    • Weak hydrophobic interactions: Between nonpolar R groups, often causing them to aggregate in the interior of the protein, away from water.

  • Stability: The tertiary structure often minimizes free energy, meaning the folded structure with the lowest free energy is the most stable conformation.

  • Prevalence: Common in globular proteins.

4. Quaternary Structure

  • Definition: Arises from interactions between multiple polypeptide units.

  • Functionality: Occurs when more than one polypeptide chain (each with its own primary, secondary, and tertiary structure) works together as a single functional macromolecule.

  • Subunits: Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein.

  • Example: Hemoglobin, which contains four subunits (polypeptide chains) working together to carry oxygen.

Complex Carbohydrates

Structure & Function in Carbohydrates

  • Composition: Carbohydrates are polymers made of sugar monomers bonded together by covalent bonds.

  • Properties & Functions: The type of monomer and the nature of the covalent bonds determine each carbohydrate's specific properties and functions.

  • Structure: Carbohydrate polymers can be linear (e.g., amylose) or branched (e.g., glycogen).

Forming a Carbohydrate

  • Process: Carbohydrate monomers (monosaccharides) join together via dehydration synthesis reactions.

  • Bond Formation: A new covalent bond forms between two monomers, holding the carbohydrate together, and a molecule of water is produced.

  • Example: Two sugar monomers (monosaccharides) join to form a simple carbohydrate (disaccharide).

Uses of Carbohydrates

  • Energy Storage:

    • Starch: In plants.

    • Glycogen: In animals.

  • Structural Uses:

    • Cellulose: In plant cell walls.

    • Chitin: In animals such as insects (exoskeletons).

  • Dietary Fiber: Many structural carbohydrates (e.g., cellulose) are largely indigestible by animals and form a significant part of the dietary fiber requirements, aiding digestive health.

  • Examiner Tip: You don't need to know precise molecular structures of sugars, but you should recognize that structure determines function and be able to infer functions from diagrams.

Lipids

Structure & Function in Lipids

  • Composition: Lipids are macromolecules composed primarily of carbon, hydrogen, and oxygen atoms.

  • Two Main Groups:

    • Triglycerides

    • Phospholipids

Triglycerides

  • Nature: Nonpolar, hydrophobic molecules.

  • Monomers: Formed from glycerol and fatty acids.

    • Glycerol: An alcohol molecule.

    • Fatty Acids: Contain a methyl group (- ext{CH}_3) at one end of a hydrocarbon chain (the R group) and a carboxyl group (- ext{COOH}) at the other end. Shorthand chemical formula: ext{RCOOH}.

  • Formation: A triglyceride is formed through a dehydration synthesis reaction.

    • Covalent bonds (ester bonds) form between the hydroxyl groups of glycerol and the carboxyl groups of the fatty acid chains.

    • For each bond formed, a water molecule is released.

    • Typically, three fatty acids join to one glycerol molecule to form a triglyceride.

Saturation of Fatty Acids

  • Fatty acids vary in:

    • The length of their hydrocarbon chain (R group).

    • The saturation of the fatty acid chain (R group), which can be saturated or unsaturated.

  • Saturation determines the structure and function of lipids.

    • Saturated Fatty Acids:

      • Contain no double bonds between the carbon atoms in the hydrocarbon chain.

      • These chains are straight.

      • Being straight allows them to pack together tightly, making these fats solid at room temperature (e.g., butter).

    • Unsaturated Fatty Acids:

      • Contain at least one carbon-carbon double bond in the hydrocarbon chain.

      • These chains have a bend or 'kink' wherever a double bond is present.

      • The bends prevent the fatty acids from packing together tightly, meaning these fats are usually liquid at room temperature (e.g., olive oil).

  • Examiner Tip: A saturated lipid is 'saturated' with hydrogen atoms, meaning it has the maximum possible number of hydrogens and no double bonds.

Functions of Lipids

  • Long-Term Energy Storage:

    • Lipids are energy-dense (contain more energy per gram than carbohydrates).

    • They are insoluble in water, which means they do not affect osmosis or upset the water balance of the organism.

    • When lipids are respired, a significant amount of metabolic water is produced compared to carbohydrates. This can serve as a dietary water source in dry environments (e.g., a camel's hump stores lipids, not water, to yield metabolic water).

  • Other Roles:

    • Physical protection: Of soft organs (e.g., visceral fat).

    • Thermal insulation: Subcutaneous fat (e.g., whale blubber).

    • Buoyancy aid: Fat is less dense than water, assisting flotation.

    • Waterproofing secretions: E.g., birds' preening glands, waxy cuticles on leaf surfaces.

    • Electrical insulation: E.g., the myelin sheath around certain nerve axons.

    • Certain photosynthetic pigments: E.g., carotenoids.

    • Glycolipids: Typically serve as cell-surface recognition molecules/receptors.

Phospholipids

  • Definition: A type of lipid distinct from triglycerides.

  • Composition: Formed from the monomer glycerol and fatty acids.

    • Unlike triglycerides, phospholipids have only two fatty acids bonded to a glycerol molecule, as one has been replaced by a phosphate ion (\text{PO}_4^{3-}).

  • Bipolar Nature:

    • The phosphate head is polar and therefore soluble in water (hydrophilic).

    • The fatty acid tails are nonpolar and, therefore, insoluble in water (hydrophobic).

    • Because they possess both hydrophobic and hydrophilic parts, phospholipid molecules are considered bipolar (or amphipathic).

  • Behavior in Water: Due to their bipolar nature, phospholipid molecules spontaneously form monolayers or (more commonly) bilayers in the presence of water.

Functions of Phospholipids

  • Main Component of Cell Membranes: Phospholipids are the fundamental building blocks of cell surface membranes (and organelle membranes).

    • The hydrophobic fatty acid tails create a barrier to water-soluble molecules, regulating what enters and exits the cell or organelle.

    • The hydrophilic phosphate heads form hydrogen bonds with water, allowing the cell membrane to be used for compartmentalization, which helps cells organize specific roles into organelles for greater efficiency.

  • Control of Membrane Fluidity: The composition of the phospholipid fatty acid tails contributes to the fluidity of the cell membrane.

    • If there are mainly saturated fatty acid tails, the membrane will be less fluid (more rigid) due to tight packing.

    • If there are mainly unsaturated fatty acid tails (with their kinks), the membrane will be more fluid due to looser packing.

  • Membrane Protein Orientation: Weak hydrophobic interactions between the phospholipids and membrane proteins hold the proteins within the membrane, but still allow movement within the lipid bilayer.

  • Examiner Tip: Ensure you know the difference between phospholipids and triglycerides.