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Chapter 3 Biological Macromolecules

Biological Macromolecules

Introduction to Organic Compounds

  • Organic compounds are the backbone of biological molecules, primarily involving carbon atoms covalently bonded to other elements, especially hydrogen, oxygen, nitrogen, sulfur, and phosphorus. They are defined by their structural diversity and complexity.

  • Carbon is unique due to its ability to form four stable covalent bonds, allowing it to serve as the "skeleton" for a vast array of molecular structures. This tetravalency enables carbon atoms to link together in diverse ways:

    • Length of carbon skeletons: Carbon chains can vary in length, from simple methane (CH4) to long hydrocarbon chains, forming the basis of molecules like butane (C4H10) or propane (C3H8).

    • Location of double bonds: The presence and position of double (or triple) bonds between carbon atoms introduce rigidity and can lead to different isomers (e.g., cis-trans isomers).

    • Branching of carbon chains: Carbon skeletons can be unbranched or branched, leading to different structural isomers with distinct properties.

    • Ring formations: Carbon atoms can form stable ring structures, such as in glucose or steroids, greatly expanding molecular diversity.

Chemical Groups

  • Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. They are often hydrophilic (water-loving):

    • Hydroxyl group (-OH): Consists of a hydrogen atom bonded to an oxygen atom, which in turn is bonded to the carbon skeleton. Compounds with hydroxyl groups are called alcohols (e.g., ethanol). They are polar due to the electronegativity of oxygen, making them hydrophilic and able to form hydrogen bonds.

    • Carbonyl group (C=O): Consists of a carbon atom double-bonded to an oxygen atom.

      • If the carbonyl group is at the end of the carbon skeleton, it is an aldehyde (e.g., propanal).

      • If the carbonyl_group is within the carbon skeleton, it is a ketone (e.g., propanone).

      • Both types are polar and found in sugars.

    • Carboxyl group (-COOH): Consists of a carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group. Compounds with carboxyl groups are called carboxylic acids (e.g., acetic acid). They are acidic because the covalent bond between oxygen and hydrogen is so polar that the hydrogen ion (H+) can dissociate reversibly, acting as a proton donor.

    • Amino group (-NH2): Consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. Compounds with amino groups are called amines (e.g., glycine). They act as a base by picking up H+ from the surrounding solution (e.g., in living organisms, water).

    • Phosphate group (-OPO3^2-): Consists of a phosphorus atom bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges. Compounds with phosphate groups are involved in energy transfer (e.g., ATP) and are components of nucleic acids and phospholipids. They are polar and acidic, releasing H+ upon dissociation.

    • Methyl group (-CH3): Consists of a carbon atom bonded to three hydrogen atoms. Methylated compounds are nonpolar and less reactive. They affect gene expression (epigenetics) by attaching to DNA or proteins bound to DNA, without altering the DNA sequence itself. They can also affect the shape and function of sex hormones.

Macromolecules

  • Macromolecules are large, complex organic molecules essential for life, typically formed by the joining of smaller molecular units.

  • Classified into four major groups:

    1. Carbohydrates

    2. Lipids

    3. Proteins

    4. Nucleic acids

  • Macromolecules are typically polymers, long molecules consisting of many similar or identical building blocks linked by covalent bonds. These building blocks are called monomers. For example, amino acids are the monomers that link together to form protein polymers.

Reactions Involving Macromolecules

  • The synthesis and breakdown of polymers involve specific chemical reactions:

    • Dehydration reactions (or dehydration synthesis): This process links monomers together. A water molecule (H_2O) is removed as two monomers are covalently bonded. One monomer contributes a hydroxyl group (-OH), and the other contributes a hydrogen atom (-H). This energetically unfavorable reaction requires energy input and is catalyzed by enzymes.

    • Hydrolysis reactions: This process breaks polymers apart into their constituent monomers. A water molecule is added to break the covalent bond linking the monomers. The hydroxyl group from water attaches to one monomer, and a hydrogen atom attaches to the other. This is an energetically favorable reaction, usually catalyzed by hydrolytic enzymes.

Carbohydrates

  • Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, typically in a ratio of CH_2O. They serve as a primary energy source and structural components.

  • Monosaccharides (simple sugars): The simplest carbohydrates, often with formulas that are multiples of CH2O (e.g., glucose, fructose, galactose, all are C6H{12}O6). They are the monomers of carbohydrates and are readily used for cellular respiration.

  • Disaccharides: Formed by joining two monosaccharides via a dehydration reaction, forming a glycosidic linkage. Common examples include:

    • Sucrose: (table sugar) formed from glucose + fructose.

    • Maltose: (malt sugar) formed from glucose + glucose.

    • Lactose: (milk sugar) formed from glucose + galactose.

  • Polysaccharides: Large carbohydrates composed of hundreds to thousands of monosaccharides linked by glycosidic bonds. They function in energy storage or structural support:

    • Starch: A storage polysaccharide in plants, providing energy. It is composed entirely of glucose monomers and is largely helical.

    • Glycogen: The major storage polysaccharide in animals, primarily stored in liver and muscle cells. It is more extensively branched than starch, allowing for quicker hydrolysis when glucose is needed.

    • Cellulose: A major structural component of plant cell walls. Also composed of glucose monomers, but the glycosidic linkages are different, preventing most animals (including humans) from digesting it. It forms strong microfibrils.

    • Chitin: A structural polysaccharide found in the exoskeletons of arthropods (insects, crustaceans) and the cell walls of fungi. It is similar to cellulose but contains nitrogen-containing appendages on its glucose monomers.

Lipids

  • Lipids are a diverse group of hydrophobic (water-fearing) molecules, meaning they do not mix well with water. They are not true polymers, as they are not built from repeating monomeric units. Their primary functions include long-term energy storage, insulation, and membrane formation.

  • Types of lipids include:

    1. Fats (Triglycerides): Composed of a glycerol molecule (a three-carbon alcohol) linked to three fatty acid molecules via ester linkages (a type of dehydration reaction). Fatty acids are long hydrocarbon chains with a carboxyl group at one end. Fats are primarily used for energy storage.

      • Saturated fats: Have no double bonds between carbon atoms in their fatty acid chains, making them "saturated" with hydrogen. They are typically solid at room temperature (e.g., butter) and primarily found in animal products. Their straight chains allow molecules to pack tightly.

      • Unsaturated fats: Contain one or more double bonds in their fatty acid chains, which often results in "kinks" in the chain. They are typically liquid at room temperature (oils, e.g., olive oil) and found in plant and fish products. These kinks prevent tight packing.

      • Trans fats: Artificially hydrogenated unsaturated fats, where hydrogen atoms are added to unsaturated fats to solidify them. The process can create trans double bonds which are uncommon in nature and are linked to increased risk of cardiovascular disease.

    2. Phospholipids: Crucial components of cell membranes. They are similar to triglycerides but have only two fatty acids attached to glycerol, with the third hydroxyl group joined to a phosphate group (which often has an additional small polar molecule attached). This structure gives them a hydrophilic (polar) head and two hydrophobic (nonpolar) tails, allowing them to form lipid bilayers in aqueous environments.

    3. Steroids: Characterized by a carbon skeleton consisting of four fused rings. Different steroids are distinguished by the chemical groups attached to this ring structure.

      • Cholesterol: A common component of animal cell membranes and a precursor from which other steroids (like sex hormones: estrogen, testosterone) are synthesized. While essential, high levels are associated with cardiovascular problems.

Proteins

  • Proteins are the most structurally and functionally diverse group of macromolecules, involved in nearly every dynamic process in living organisms. They are polymers of amino acids.

  • Composed of amino acids: Organic molecules possessing both an amino group (-NH2) and a carboxyl group (-COOH). All amino acids also have a central carbon atom (alpha carbon) bonded to a hydrogen atom and a variable side chain (R group).

    • There are 20 different common amino acids, each with a unique R group that determines its chemical properties (e.g., nonpolar, polar, acidic, basic).

  • Peptide bonds: Amino acids are linked together by peptide bonds, formed via dehydration reactions between the carboxyl group of one amino acid and the amino group of another. A chain of amino acids is called a polypeptide.

  • Proteins perform various functions:

    • Enzymatic: Act as catalysts, accelerating biochemical reactions (e.g., digestive enzymes).

    • Structural: Provide support and shape (e.g., collagen in connective tissues, keratin in hair).

    • Transport: Carry substances (e.g., hemoglobin transports oxygen).

    • Defense: Protect against disease (e.g., antibodies).

    • Hormonal: Coordinate organismal activities (e.g., insulin).

    • Motor: Function in movement (e.g., actin and myosin).

    • Storage: Store amino acids (e.g., casein in milk).

  • Proteins have four hierarchical structural levels, crucial for their function:

    1. Primary structure: The unique linear sequence of amino acids in a polypeptide chain. This sequence is determined by genetic information and dictates all subsequent structural levels.

    2. Secondary structure: Localized folding patterns within parts of the polypeptide chain, stabilized by hydrogen bonds between atoms of the polypeptide backbone (not the R groups). Common forms include:

      • Alpha (\alpha) helix: A delicate coil held together by hydrogen bonding between every fourth amino acid.

      • Beta (\beta) pleated sheet: Consists of two or more segments of the polypeptide chain lying side by side, connected by hydrogen bonds.

    3. Tertiary structure: The overall three-dimensional shape of a single polypeptide chain, resulting from interactions between the R groups of the amino acids. These interactions include hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges (covalent bonds between two cysteine R groups).

    4. Quaternary structure: Arises when a protein consists of two or more polypeptide chains (subunits) that associate to form a functional macromolecule. Examples include hemoglobin (four subunits) and collagen (three subunits).

  • Denaturation: The process by which a protein loses its native shape (and thus its biological activity) due to the disruption of its secondary, tertiary, and quaternary structures. This can be caused by changes in pH, temperature, salt concentration, or exposure to certain chemicals. Denaturation can be irreversible.

Nucleic Acids

  • Nucleic acids are polymers that store, transmit, and express hereditary information. Their monomers are nucleotides.

  • Composed of nucleotides: Each nucleotide consists of three components:

    1. A five-carbon sugar (pentose)

    2. A phosphate group

    3. A nitrogenous base

  • There are two main types of nucleic acids:

    • DNA (deoxyribonucleic acid): Typically a double helix structure (two polynucleotide strands coiled around a common axis). It stores the genetic information for an organism. The backbone is formed by sugar-phosphate linkages, with nitrogenous bases projecting inward. Base pairing occurs between complementary bases via hydrogen bonds: adenine (A) always pairs with thymine (T), and guanine (G) always pairs with cytosine (C).

    • RNA (ribonucleic acid): Typically single-stranded. It is involved in various aspects of gene expression, especially protein synthesis. In RNA, uracil (U) replaces thymine (T), so adenine (A) pairs with uracil (U), and guanine (G) pairs with cytosine (C). There are different types of RNA, each with specific roles (e.g., messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA)).

  • The Central Dogma of molecular biology describes the flow of genetic information: DNA contains the genetic instructions, which are transcribed into RNA, and then translated into protein. This is summarized as: DNA \rightarrow RNA \rightarrow Protein.

Lactose Tolerance

  • Lactose tolerance represents a relatively recent human genetic mutation that allows adults to continue producing lactase, the enzyme required to digest lactose (the sugar in milk), beyond infancy. This mutation, known as lactase persistence, is particularly prevalent in populations with a long history of dairy farming.

  • For individuals without this mutation, lactase production typically declines after weaning, leading to lactose intolerance, where undigested lactose ferments in the gut, causing discomfort.

  • This genetic adaptation highlights how environmental factors (like the availability of milk) can drive evolutionary changes in human populations.