The Structure and Function of Large Biological Molecules

The Molecules of Life

• All living things are composed of four main classes of large biological molecules:

  • Carbohydrates

  • Lipids

  • Proteins

  • Nucleic acids

• Macromolecules are large, complex molecules.

• Large biological molecules possess unique properties derived from the ordered arrangement of their constituent atoms.

Macromolecules: Polymers Built from Monomers

• Polymer: A long molecule composed of many similar or identical building blocks linked by covalent bonds.

• Monomer: The repeating units that serve as the building blocks of a polymer.

• Three of the four classes of life’s organic molecules are polymers:

  • Carbohydrates

  • Proteins

  • Nucleic acids

• Lipids are the exception; they are not polymers and are generally not considered macromolecules in the same way, though they are large biological molecules.

Synthesis and Breakdown of Polymers

• Enzymes: Specialized macromolecules (usually proteins) that function as catalysts to speed up chemical reactions, including those that build or break down polymers.

• Dehydration Reaction (Synthesis):

  • Occurs when two monomers are covalently bonded together.

  • Involves the loss of a water molecule ($H_2O$).

  • Forms a new covalent bond between the monomers.

• Hydrolysis (Breakdown):

  • The process by which polymers are disassembled into monomers.

  • Essentially the reverse of a dehydration reaction.

  • A water molecule ($H_2O$) is added, breaking a covalent bond in the polymer.

Diversity of Polymers

• Each cell contains thousands of different macromolecules.

• Macromolecules exhibit variation:

  • Among different cells within an organism.

  • More significant variation within a species.

  • Even greater variation between different species.

• A vast array of polymers can be constructed from a relatively small set of monomers, much like a few letters of the alphabet form countless words.

Carbohydrates: Fuel and Building Material

• Carbohydrates encompass sugars and the polymers formed from sugars.

Sugars

• Monosaccharides (Simple Sugars):

  • The simplest carbohydrates.

  • Typically have molecular formulas that are multiples of $CH_2O$.

  • Glucose ($C<em>6H</em>{12}O_6$) is the most common monosaccharide.

  • Classification:

    • Location of the carbonyl group:

      • Aldose (aldehyde sugar): Carbonyl group at the end of the carbon skeleton (e.g., Glyceraldehyde, Ribose, Glucose, Galactose).

      • Ketose (ketone sugar): Carbonyl group within the carbon skeleton (e.g., Dihydroxyacetone, Ribulose, Fructose).

    • Number of carbons in the carbon skeleton:

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

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

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

  • In aqueous solutions, many sugars form ring structures rather than remaining in linear skeletons.

  • Serve as a major fuel for cellular respiration and as raw material for synthesizing other organic molecules (e.g., in metabolic pathways).

• Disaccharides:

  • Formed when two monosaccharides are joined by a dehydration reaction.

  • The covalent bond connecting them is called a glycosidic linkage.

  • Examples:

    • Maltose: Glucose + Glucose, linked by a $1-4$ glycosidic linkage.

    • Sucrose: Glucose + Fructose, linked by a $1-2$ glycosidic linkage (table sugar).

Polysaccharides

• Polymers of many sugar building blocks (monosaccharides).

• Serve significant storage and structural roles.

  • The specific architecture and function of a polysaccharide are determined by its sugar monomers and the positions of its glycosidic linkages.

• Storage Polysaccharides:

  • Starch:

    • The primary storage polysaccharide in plants.

    • Consists entirely of glucose monomers.

    • Plants store surplus starch as granules within chloroplasts and other plastids.

    • The simplest form is amylose (unbranched).

    • Amylopectin is a more complex, somewhat branched form.

    • The glucose monomers in starch are joined by $\alpha$ glycosidic linkages, causing the polymer to be largely helical in structure.

  • Glycogen:

    • The main storage polysaccharide in animals.

    • Extensively branched polymer of glucose.

    • Primarily stored in liver and muscle cells.

    • Hydrolysis of glycogen in these cells releases glucose rapidly when the demand for sugar (energy) increases (e.g., during exercise or fasting).

• Structural Polysaccharides:

  • Cellulose:

    • A major component of the tough plant cell walls.

    • Like starch, it is a polymer of glucose.

    • However, the glycosidic linkages differ: cellulose uses $\beta$ glycosidic linkages (as opposed to $\alpha$ in starch).

    • Glucose ring forms: The difference is based on two ring forms for glucose which are in equilibrium in aqueous solution: alpha ($\alpha$) glucose and beta ($\beta$) glucose.

    • Cellulose molecules (with $\beta$ configuration) are straight and unbranched.

    • Many hydroxyl groups ($-OH$) on parallel cellulose molecules can form hydrogen bonds with each other, leading to the formation of strong microfibrils.

    • Digestibility: Enzymes that digest starch by hydrolyzing $\alpha$ linkages cannot hydrolyze the $\beta$ linkages in cellulose due to the structural difference.

      • Humans cannot digest cellulose; it passes through the digestive tract as "insoluble fiber," which aids in digestion.

      • Some microbes (e.g., in the guts of cows, termites) possess enzymes to digest cellulose, forming symbiotic relationships with these herbivores.

  • Chitin:

    • Another important structural polysaccharide.

    • Found in the tough exoskeletons of arthropods (insects, crustaceans).

    • Also provides structural support for the cell walls of many fungi.

    • Has practical applications, such as being used to make strong and flexible surgical thread.

Lipids: Diverse Hydrophobic Molecules

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

• Unifying feature: They mix poorly, if at all, with water; hence, they are hydrophobic.

• Their hydrophobicity arises because they consist mostly of hydrocarbons, which form nonpolar covalent bonds.

• The most biologically important lipids are fats, phospholipids, and steroids.

Fats

• Constructed from two types of smaller molecules:

  • Glycerol: A three-carbon alcohol with a hydroxyl group ($-OH$) attached to each carbon.

  • Fatty acids: Consist of a carboxyl group ($-COOH$) at one end attached to a long carbon skeleton (hydrocarbon chain).

• When forming a fat, three fatty acids are joined to glycerol by ester linkages via dehydration reactions.

• The resulting molecule is called a triacylglycerol or triglyceride.

• Fats separate from water because water molecules hydrogen-bond to each other, excluding the nonpolar fat molecules.

• Fatty acids within a single fat molecule can be all the same or of two or three different kinds.

• Variation in Fatty Acids:

  • Vary in length (number of carbons).

  • Vary in the number and locations of double bonds.

  • Saturated Fatty Acids:

    • Have the maximum number of hydrogen atoms possible, meaning no double bonds between carbon atoms in the hydrocarbon chain.

    • Fats made from saturated fatty acids are called saturated fats and are typically solid at room temperature (e.g., most animal fats).

    • A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits in blood vessels.

  • Unsaturated Fatty Acids:

    • Have one or more double bonds between carbon atoms in the hydrocarbon chain.

    • The double bonds often cause kinks or bends in the hydrocarbon chain (specifically, cis double bonds).

    • Fats made from unsaturated fatty acids are called unsaturated fats or oils and are typically liquid at room temperature (e.g., plant fats, fish fats).

  • Hydrogenation:

    • A process that converts unsaturated fats to saturated fats by adding hydrogen atoms, thereby breaking double bonds and creating single bonds.

    • This process can also create trans double bonds in unsaturated fats, resulting in trans fats.

    • Trans fats are considered particularly unhealthy and may contribute more to cardiovascular disease than saturated fats.

  • Essential Fatty Acids:

    • Certain unsaturated fatty acids that the human body cannot synthesize.

    • Must be obtained from the diet.

    • Omega-$3$ fatty acids are an example, required for normal growth and potentially offering protection against cardiovascular disease.

• Major Function of Fats: Energy storage.

  • Humans and other mammals store long-term food reserves in adipose cells.

  • Adipose tissue also serves to cushion vital organs and insulate the body.

Phospholipids

• In a phospholipid, two fatty acids and a phosphate group are attached to glycerol.

• Structure:

  • The two fatty acid tails are hydrophobic (water-fearing).

  • The phosphate group and its attachments form a hydrophilic head (water-loving).

  • This amphipathic nature (both hydrophilic and hydrophobic parts) is crucial for their function.

• When phospholipids are added to water, they spontaneously self-assemble into double-layered structures called bilayers.

• At the surface of a cell, phospholipids are arranged in a bilayer, with the hydrophobic tails pointing towards the interior of the membrane and the hydrophilic heads facing the aqueous environment inside and outside the cell.

• The unique structure of phospholipids is fundamental to the formation of cell membranes, and thus, the existence of cells depends on them.

Steroids

• Lipids characterized by a carbon skeleton consisting of four fused rings.

• Cholesterol:

  • A type of steroid that is an essential component in animal cell membranes.

  • Serves as a precursor from which other steroids (e.g., sex hormones) are synthesized.

  • High levels of cholesterol in the blood may contribute to cardiovascular disease.

Proteins: Diversity of Structures and Functions

• Proteins are the most structurally and functionally diverse molecules, accounting for more than $50\%$ of the dry mass of most cells.

• Diverse Functions of Proteins:

  • Enzymatic proteins: Selective acceleration of chemical reactions (e.g., digestive enzymes catalyzing hydrolysis of food bonds).

  • Storage proteins: Storage of amino acids (e.g., casein in milk, ovalbumin in egg white, plant seed proteins).

  • Defensive proteins: Protection against disease (e.g., antibodies inactivating viruses and bacteria).

  • Transport proteins: Transport of substances (e.g., hemoglobin transports oxygen; membrane proteins transport molecules across cell membranes).

  • Hormonal proteins: Coordination of an organism’s activities (e.g., insulin regulates blood sugar concentration).

  • Receptor proteins: Response of cells to chemical stimuli (e.g., nerve cell receptors detecting signaling molecules).

  • Contractile and motor proteins: Movement (e.g., actin and myosin in muscle contraction; motor proteins responsible for cilia and flagella undulations).

  • Structural proteins: Support (e.g., keratin in hair/horns/feathers; silk fibers in cocoons/webs; collagen and elastin in animal connective tissues).

• Enzymes are proteins that act as catalysts to speed up specific chemical reactions without being consumed in the process.

  • They can perform their functions repeatedly, acting as essential "workhorses" of life.

Amino Acid Polymers (Polypeptides)

• All proteins are constructed from the same set of $20$ amino acids.

• Polypeptides are unbranched polymers built from these amino acids.

• A protein is a biologically functional molecule consisting of one or more polypeptides.

• Amino Acid Structure:

  • Each amino acid consists of a central $\alpha$ carbon atom bonded to:

    • An amino group ($NH_2$)

    • A carboxyl group ($COOH$)

    • A hydrogen atom ($H$)

    • A variable side chain, designated R group

• Classification of Amino Acids by R Group Properties:

  • Nonpolar side chains (hydrophobic): e.g., Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Tryptophan, Phenylalanine, Methionine.

  • Polar side chains (hydrophilic): e.g., Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine.

  • Electrically charged side chains (hydrophilic):

    • Acidic (negatively charged): e.g., Aspartic acid, Glutamic acid.

    • Basic (positively charged): e.g., Lysine, Arginine, Histidine.

• Peptide Bonds:

  • Amino acids are linked together by covalent bonds called peptide bonds.

  • Formed via a dehydration reaction between the carboxyl group of one amino acid and the amino group of another.

• Polypeptide Characteristics:

  • Range in length from a few monomers to more than a thousand.

  • Each polypeptide has a unique linear sequence of amino acids.

  • Has a distinct amino end (N-terminus) with a free amino group and a carboxyl end (C-terminus) with a free carboxyl group.

Protein Structure and Function

• The specific activities of proteins are a direct result of their intricate three-dimensional architecture.

• A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique, biologically active shape.

• The sequence of amino acids (primary structure) ultimately determines a protein’s 3D structure.

• A protein’s structure dictates how it works; its function usually depends on its ability to recognize and bind to some other molecule with specificity (e.g., an antibody binding to a virus protein).

Four Levels of Protein Structure

• 1. Primary Structure ($1^{\circ}$):

  • The unique linear sequence of amino acids in a polypeptide chain.

  • This sequence is like the order of letters in a very long word.

  • It is determined by inherited genetic information.

• 2. Secondary Structure ($2^{\circ}$):

  • Consists of coils and folds in the polypeptide chain.

  • These structures result from hydrogen bonds formed between the repeating constituents of the polypeptide backbone (not the R groups).

  • Typical secondary structures include:

    • The $\alpha$ (alpha) helix: a delicate coil, stabilized by hydrogen bonds between every fourth amino acid.

    • The $\beta$ (beta) pleated sheet: a folded, accordion-like structure formed by hydrogen bonds between parallel segments of the polypeptide backbone.

• 3. Tertiary Structure ($3^{\circ}$):

  • The overall three-dimensional shape of a polypeptide.

  • Determined by interactions among the R groups (side chains) of the amino acids, rather than interactions between backbone constituents.

  • These interactions can include:

    • Hydrogen bonds between polar side chains.

    • Ionic bonds between charged (acidic and basic) side chains.

    • Hydrophobic interactions and van der Waals interactions between nonpolar side chains clustered in the protein's core.

  • Strong covalent bonds called disulfide bridges ($-S-S-$) may form between the sulfhydryl groups of two cysteine monomers, further reinforcing the protein’s structure.

• 4. Quaternary Structure ($4^{\circ}$):

  • Arises when a protein consists of two or more polypeptide chains that aggregate to form one functional macromolecule.

  • Examples:

    • Collagen: A fibrous protein composed of three polypeptides coiled together like a rope, providing connective tissue strength.

    • Hemoglobin: A globular protein consisting of four polypeptide subunits: two alpha ($\alpha$) chains and two beta ($\beta$) chains, each binding a heme group with iron to transport oxygen.

Sickle-Cell Disease: A Change in Primary Structure

• A slight alteration in a protein’s primary structure can profoundly affect its overall structure and biological function.

• Sickle-cell disease is an inherited blood disorder.

  • It results from a single amino acid substitution (glutamic acid to valine) in the primary structure of the $\beta$ subunit of the protein hemoglobin.

  • This change causes hemoglobin molecules to aggregate into fibers under low oxygen conditions, reducing their oxygen-carrying capacity and deforming red blood cells into a sickle shape ($5 \text{ µm}$).

What Determines Protein Structure?

• Beyond primary amino acid sequence, physical and chemical conditions significantly affect protein structure.

• Denaturation:

  • The loss of a protein’s native (biologically active) structure (unraveling).

  • Caused by alterations in environmental factors such as:

    • pH (changes in $H^+$ concentration)

    • Salt concentration (disrupting ionic bonds)

    • Temperature (excessive heat can disrupt weak bonds)

    • Exposure to certain chemicals

  • A denatured protein is biologically inactive and usually cannot perform its function.

• Renaturation: In some cases, if the denaturing agent is removed, a protein may spontaneously refold back into its correct functional shape.

Protein Folding in the Cell

1. It is challenging to predict a protein’s final $3D$ structure solely from its primary amino acid sequence.

2. Most proteins likely proceed through several intermediate stages on their way to a stable, functional structure.

3. Chaperonins (Chaperone Proteins):

   • Protein molecules that assist the proper folding of other proteins.

   • They provide a protective environment for polypeptide folding, preventing aggregation or incorrect folding.

   • Mechanism: An unfolded polypeptide enters a hollow cylinder; a cap attaches, creating a hydrophilic environment inside for folding; the cap comes off, and the properly folded protein is released.

4. Misfolded proteins are associated with serious diseases, including Alzheimer’s disease, Parkinson’s disease, and mad cow disease.

• Methods for Determining Protein Structure:

  • X-ray crystallography: Often used to determine the precise three-dimensional structure of a crystallized protein by analyzing the diffraction pattern of X-rays.

  • Nuclear Magnetic Resonance (NMR) spectroscopy: Another method that can determine protein structure, which has the advantage of not requiring protein crystallization.

  • Bioinformatics: Computational approaches used to predict protein structure from amino acid sequences, especially valuable for large-scale analysis.

Nucleic Acids: Store, Transmit, and Express Hereditary Information

• The amino acid sequence of a polypeptide is ultimately programmed by a unit of inheritance called a gene.

• Genes are composed of DNA (deoxyribonucleic acid), which is a type of nucleic acid.

• The monomers of nucleic acids are nucleotides.

The Roles of Nucleic Acids

• There are two main types of nucleic acids:

  • Deoxyribonucleic acid (DNA)

  • Ribonucleic acid (RNA)

• DNA’s Functions:

  • Provides directions for its own replication when a cell divides.

  • Directs the synthesis of messenger RNA (mRNA).

  • Through mRNA, DNA ultimately controls protein synthesis.

• This entire process from gene to protein is called gene expression.

• Flow of Genetic Information (Central Dogma):

  1. DNA synthesis of mRNA (Transcription): A gene along a DNA molecule serves as a template for the synthesis of a complementary mRNA molecule within the nucleus.

  2. Movement of mRNA into cytoplasm.

  3. mRNA directs synthesis of protein (Translation): The mRNA molecule interacts with the cell’s protein-synthesizing machinery (ribosomes) in the cytoplasm to direct the production of a specific polypeptide.

  • Summarized as: $DNA \rightarrow RNA \rightarrow protein$

The Components of Nucleic Acids

• Nucleic acids are polymers known as polynucleotides.

• Each polynucleotide is made up of monomers called nucleotides.

• Each nucleotide consists of three parts:

  • A nitrogenous base

  • A pentose sugar ($5$-carbon sugar)

  • One or more phosphate groups

• A nucleoside is the portion of a nucleotide without the phosphate group (i.e., nitrogenous base + sugar).

• Nitrogenous Bases (two families):

  • Pyrimidines: Characterized by a single six-membered carbon-nitrogen ring.

    • Cytosine (C)

    • Thymine (T) (found only in DNA)

    • Uracil (U) (found only in RNA, replaces Thymine)

  • Purines: Characterized by a six-membered ring fused to a five-membered ring.

    • Adenine (A)

    • Guanine (G)

• Pentose Sugars:

  • In DNA: The sugar is deoxyribose (it lacks an oxygen atom on the $2^{\prime}$ carbon compared to ribose).

  • In RNA: The sugar is ribose.

Nucleotide Polymers

• Nucleotides are linked together to construct a polynucleotide chain.

• Adjacent nucleotides are joined by a phosphodiester linkage.

  • This linkage consists of a phosphate group that covalently links the $5^{\prime}$ carbon of one sugar to the $3^{\prime}$ carbon of the next sugar.

• These links create a repeating sugar-phosphate backbone along the polynucleotide, with the nitrogenous bases as appendages.

• A polynucleotide has a distinct $5^{\prime}$ end (with a free phosphate group attached to the $5^{\prime}$ carbon of the sugar) and a $3^{\prime}$ end (with a free hydroxyl group attached to the $3^{\prime}$ carbon of the sugar).

• The specific sequence of bases along a DNA or mRNA polymer is unique for each gene and carries the genetic information.

The Structures of DNA and RNA Molecules

• DNA (Deoxyribonucleic Acid):

  • Typically exists as a double helix, consisting of two polynucleotides spiraling around an imaginary central axis.

  • The two sugar-phosphate backbones run in antiparallel directions to each other (one strand runs $5^{\prime} \rightarrow 3^{\prime}$ and the other runs $3^{\prime} \rightarrow 5^{\prime}$).

  • One DNA molecule includes many genes.

  • Complementary Base Pairing: Only specific pairs of nitrogenous bases can form hydrogen bonds and interact with each other in the double helix:

    • Adenine (A) always pairs with Thymine (T).

    • Guanine (G) always pairs with Cytosine (C).

  • This complementary base pairing is essential for replicating DNA into two identical copies when a cell prepares to divide.

• RNA (Ribonucleic Acid):

  • In contrast to DNA, RNA molecules are generally single-stranded.

  • Base Pairing in RNA: While single-stranded, complementary pairing can still occur between regions of the same RNA molecule (forming complex $3D$ shapes, e.g., in transfer RNA, tRNA) or between two different RNA molecules.

  • In RNA, Uracil (U) replaces Thymine (T), so Adenine (A) pairs with Uracil (U).

  • RNA molecules are more variable in form and can adopt diverse three-dimensional structures depending on their function.

Genomics and Proteomics: Transforming Biological Inquiry

• Following the elucidation of DNA structure and its relationship to amino acid sequences, biologists began decoding genes by determining their base sequences.

• The first chemical techniques for DNA sequencing were developed in the $1970s$ and refined over the next $20$ years.

• The ability to sequence the full complement of DNA in an organism’s genome (all of its genetic material) has been immensely enlightening.

  • The rapid development of faster and less expensive sequencing methods was significantly spurred by the Human Genome Project.

  • Many genomes have now been sequenced, generating vast amounts of biological data.

• Bioinformatics: An interdisciplinary field that utilizes computer software and other computational tools to manage, analyze, and interpret the enormous datasets generated from sequencing many genomes.

• Genomics: The systematic study and comparison of large sets of genes, or even entire genomes, of different species.

• Proteomics: A similar large-scale analysis of sets of proteins, including their sequences, structures, and functions.

DNA and Proteins as Tape Measures of Evolution

• The sequences of genes and their protein products serve as a molecular record, documenting the hereditary background of an organism.

• Linear sequences of DNA molecules are faithfully passed from parents to offspring.

• The concept of tracing "molecular genealogy" can be extended to understand the evolutionary relationships between different species by comparing their DNA and protein sequences.

• Molecular biology, through genomics and proteomics, has added a powerful new measure to the toolkit of evolutionary biology, allowing for precise comparisons at the molecular level.