Study Guide: Large Biological Molecules

Chemistry of Life: Large Molecules

Chapter 5: The Structure and Function of Large Biological Molecules

Overview

• Large biological molecules, also known as macromolecules, play a crucial role in the properties of cells.

• Four primary classes of macromolecules:

  • Carbohydrates

  • Proteins

  • Nucleic acids

  • Lipids

• Macromolecules are characterized by unique properties that stem from the orderly arrangement of their atoms, leading to what are known as "emergent properties."

Concept 5.1: Macromolecules as Polymers

• Definition: A polymer is a long molecule consisting of many similar building blocks, called monomers.

• Classes of Macromolecules as Polymers:

  • Carbohydrates: Composed of sugar monomers (saccharides).

  • Proteins: Composed of amino acid monomers.

  • Nucleic Acids: Composed of nucleotide monomers.

Dynamics of Polymers

• Synthesis of Polymers:

  • Occurs through a dehydration reaction, where a water molecule is removed to form a new bond.

  • 
    $ext{H}_2 ext{O}$ is released in the process.

• Breakdown of Polymers:

  • Occurs through hydrolysis, where the addition of a water molecule breaks bonds within the polymer.

  • Typically, these reactions require enzymes as catalysts.

Diversity of Polymers

• Each cell contains thousands of different macromolecules.

• The variation in macromolecules:

  • Varies among cells of an organism.

  • Varies even more within species and different species.

• A wide variety of polymers can be synthesized from a small set of monomers.

• Example Discussion: Determine how many water molecules are needed to hydrolyze a polymer that is 10 monomers long (Answer: 9 water molecules, since one water molecule is needed for each bond broken).

Concept 5.2: Carbohydrates

Overview

• Definition: Carbohydrates include both sugars and their polymer forms.

  • Monosaccharides: Simple sugars (e.g., glucose).

  • Polysaccharides: Long chains of monosaccharides.

Composition of Carbohydrates

• Monosaccharides generally conform to the formula of multiples of $ext{C}<em>n( ext{H}</em>2 ext{O})$.

• Common monosaccharides include those ranging in carbon count from 3 to 6:

  • Glucose ($ext{C}<em>6 ext{H}</em>{12} ext{O}_6$) - Most common monosaccharide.

• Classification of Monosaccharides:

  • Aldoses: Contain an aldehyde group (e.g., Glucose).

  • Ketoses: Contains a ketone group (e.g., Fructose).

  • Trioses: 3-carbon sugars (e.g., Glyceraldehyde).

  • Pentoses: 5-carbon sugars (e.g., Ribose).

  • Hexoses: 6-carbon sugars (e.g., Galactose, Fructose).

• Structure varies due to:

  • Number of carbons.

  • Position of carbonyl group and hydroxyl groups; these small differences significantly impact function.

Formation of Carbohydrates

• Disaccharides: Two monosaccharides connected by a glycosidic linkage (e.g., maltose formed by glucose + glucose).

• Polysaccharides: Macromolecules composed of hundreds to thousands of monosaccharide units joined by glycosidic linkages.

Functions of Carbohydrates

• Monosaccharides serve as:

  • Quick energy sources for cells.

  • Building blocks for longer polymers utilized for energy storage and structural purposes.

• Polysaccharides have various roles:

  • Storage Polysaccharides:

  • Starch (plants), a polymer form of glucose, stored in plastids for energy.

  • Glycogen (animals), primarily found in the liver and muscles, readily provides glucose when energy is required.

  • Structural Polysaccharides:

  • Cellulose: Major component of the plant cell wall, structured for rigidity.

  • Chitin: Found in insect exoskeletons and fungal cell walls.

Digestion of Polysaccharides

• Difference in glycosidic linkages between starch and cellulose requires different enzymes for hydrolysis.

  • Starch has $\beta(1 o 4)$ linkages while cellulose has $\beta(1 o 4)$ linkages with alternating orientations (helical vs. straight chain).

• In humans, cellulose appears as dietary fiber and is not easily digestible but is beneficial for digestive health.

• Symbiotic relationships exist, as certain microbes harbor enzymes that can digest cellulose for herbivores.

Summary Points:

• Carbohydrates serve essential structural and energy functions in living organisms:

  • They’re vital in energy storage and providing readily available energy for cellular processes.

Chemistry of Life: Large Molecules

Chapter 5: The Structure and Function of Large Biological Molecules

Overview

• Large biological molecules, also known as macromolecules, play a crucial role in the properties of cells.

• Four primary classes of macromolecules:

  • Carbohydrates

  • Proteins

  • Nucleic acids

  • Lipids

• Macromolecules are characterized by unique properties that stem from the orderly arrangement of their atoms, leading to what are known as "emergent properties."

Concept 5.1: Macromolecules as Polymers

• Definition: A polymer is a long molecule consisting of many similar building blocks, called monomers.

• Classes of Macromolecules as Polymers:

  • Carbohydrates: Composed of sugar monomers (saccharides).

  • Proteins: Composed of amino acid monomers.

  • Nucleic Acids: Composed of nucleotide monomers.

Dynamics of Polymers

• Synthesis of Polymers:

  • Occurs through a dehydration reaction, where a water molecule is removed to form a new bond.

  • $H_2O$ is released in the process.

• Breakdown of Polymers:

  • Occurs through hydrolysis, where the addition of a water molecule breaks bonds within the polymer.

  • Typically, these reactions require enzymes as catalysts.

Diversity of Polymers

• Each cell contains thousands of different macromolecules.

• The variation in macromolecules varies among cells of an organism and even more within and between different species.

• A wide variety of polymers can be synthesized from a small set of monomers.

• Example Discussion: To hydrolyze a polymer that is 10 monomers long, 9 water molecules are needed.

Concept 5.2: Carbohydrates

Overview

• Definition: Carbohydrates include both sugars and their polymer forms.

  • Monosaccharides: Simple sugars (e.g., glucose).

  • Polysaccharides: Long chains of monosaccharides.

Composition of Carbohydrates

• Monosaccharides generally conform to the formula of multiples of $C<em>n(H</em>2O)$.

• Common monosaccharides range in carbon count from 3 to 6:

  • Glucose ($C<em>6H</em>{12}O_6$): Most common monosaccharide.

• Classification of Monosaccharides:

  • Aldoses: Contain an aldehyde group.

  • Ketoses: Contains a ketone group.

  • Hexoses: 6-carbon sugars (e.g., Glucose, Fructose).

• Structure varies due to the number of carbons and the position of carbonyl and hydroxyl groups.

Functions of Carbohydrates

• Storage Polysaccharides:

  • Starch (plants): Stored in plastids for energy.

  • Glycogen (animals): Stored in liver and muscles for glucose provision.

• Structural Polysaccharides:

  • Cellulose: Structural component of plant cell walls.

  • Chitin: Structural component in insect exoskeletons and fungal cell walls.

Concept 5.3: Lipids

• General Characteristics:

  • Lipids are the only class of large biological molecules that do not consist of true polymers.

  • They are hydrophobic, consisting mostly of hydrocarbon regions.

• Fats:

  • Composed of glycerol and fatty acids.

  • Saturated Fatty Acids: No double bonds; maximum number of hydrogen atoms.

  • Unsaturated Fatty Acids: One or more double bonds.

• Phospholipids:

  • Consist of two fatty acids and a phosphate group; essential for cell membranes (bilayer).

• Steroids:

  • Lipids with a carbon skeleton consisting of four fused rings (e.g., Cholesterol).

Concept 5.4: Proteins

• Overview: Proteins account for more than 50% of the dry mass of most cells and are instrumental in almost everything organisms do.

• Polypeptides: Polymers built from the same set of 20 amino acids.

• Protein Structure:

  1. Primary: Sequence of amino acids.

  2. Secondary: Coils ($\alpha$-helix) and folds ($\beta$-pleated sheet).

  3. Tertiary: Overal shape of a polypeptide resulting from R group interactions.

  4. Quaternary: Overall protein structure resulting from the aggregation of polypeptide subunits.

Concept 5.5: Nucleic Acids

• Role: Store, transmit, and help express hereditary information.

• Components: Polynucleotides made of nucleotide monomers.

• Nucleotide Structure: Consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups.

• DNA vs. RNA:

  • DNA: Provides directions for its own replication; double-stranded helix.

  • RNA: Functions in protein synthesis; usually single-stranded.

Concept 5.1: Macromolecules as Polymers

• Mechanisms of Synthesis and Breakdown:

  • Dehydration Reaction: This occurs when two monomers bond together through the loss of a water molecule. One monomer provides a hydroxyl group ($-OH$), while the other provides a hydrogen ($-H$). This process is facilitated by enzymes, specialized macromolecules that speed up chemical reactions.

  • Hydrolysis: This is the reverse of dehydration. The bond between monomers is broken by the addition of a water molecule, with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other. An example is digestion: enzymes attack large polymers to release monomers that can be absorbed into the bloodstream.

Concept 5.2: Carbohydrates

• Monosaccharides and Disaccharides:

  • Glucose ($C<em>6H</em>{12}O_6$): The most common monosaccharide. Its structure includes a carbonyl group and multiple hydroxyl groups. Depending on the location of the carbonyl group, the sugar is either an aldose (aldehyde sugar) or a ketose (ketone sugar).

  • Glycosidic Linkage: A covalent bond formed between two monosaccharides by a dehydration reaction. For example, sucrose (table sugar) is formed from glucose and fructose.

  • Polysaccharide Structure and Function:

  • Storage: Plants store Starch as granules within cellular structures known as plastids. Starch consists entirely of glucose monomers joined by $\alpha$ glycosidic linkages. Animals store Glycogen, which is more extensively branched than starch, allowing for rapid release of glucose when energy demand increases.

  • Structure: Cellulose is a major component of plant cell walls. Unlike starch, it uses $\beta$ glycosidic linkages, making every other glucose monomer "upside down." This straight, unbranched structure allows cellulose molecules to group into microfibrils, providing high tensile strength.

Concept 5.3: Lipids

• Fats (Triacylglycerols):

  • Constructed from one glycerol molecule and three fatty acids. The linkage formed is an ester linkage, created by a dehydration reaction between a hydroxyl group and a carboxyl group.

  • Saturated vs. Unsaturated: Saturated fatty acids have no double bonds and are packed tightly (solid at room temperature). Unsaturated fatty acids have one or more "cis" double bonds, creating a kink in the hydrocarbon chain that prevents tight packing (liquid at room temperature).

• Phospholipids:

  • These have two fatty acids and a phosphate group attached to glycerol. They are amphipathic, meaning they have a hydrophilic (polar) head and hydrophobic (nonpolar) tails. In water, they self-assemble into a bilayer, shielding the tails from water; this is the fundamental structure of all cell membranes.

• Steroids:

  • Characterized by a carbon skeleton consisting of four fused rings. Cholesterol is a crucial steroid in animals, serving as a component of cell membranes and a precursor for other steroids like vertebrate sex hormones.

Concept 5.4: Proteins

• Amino Acids and Polypeptides:

  • Amino acids are organic molecules with both an amino group and a carboxyl group. The center is an asymmetric carbon called the $\alpha$ carbon. The R group (side chain) determines the unique characteristics of each amino acid (polar, nonpolar, acidic, or basic).

  • Peptide Bonds: Link amino acids together via dehydration reactions.

• Four Levels of Protein Structure:

  1. Primary Structure: The unique linear sequence of amino acids.

  2. Secondary Structure: Coils and folds resulting from hydrogen bonds between the polypeptide backbone. Common types include the $\alpha$-helix and the $\beta$-pleated sheet.

  3. Tertiary Structure: The overall three-dimensional shape resulting from interactions between R groups, such as hydrogen bonds, ionic bonds, hydrophobic interactions, and strong covalent disulfide bridges.

  4. Quaternary Structure: Arises when two or more polypeptide chains aggregate into one functional macromolecule (e.g., hemoglobin or collagen).

Concept 5.5: Nucleic Acids

• Structure of Nucleic Acids:

  • Nucleic acids are polymers called polynucleotides. Each monomer consists of a nitrogenous base, a five-carbon sugar (pentose), and one or more phosphate groups.

  • Nitrogenous Bases:

  • Pyrimidines: Cytosine (C), Thymine (T), and Uracil (U). These have a single six-membered ring.

  • Purines: Adenine (A) and Guanine (G). These have a six-membered ring fused to a five-membered ring.

• DNA and RNA:

  • DNA contains deoxyribose sugar and is double-stranded, forming a double helix. The two backbones run in opposite $5' \to 3'$ directions, a setup referred to as antiparallel.

  • RNA contains ribose sugar and is usually single-stranded. In RNA, thymine is replaced by uracil (U).