The Structure and Function of Large Biological Molecules
Key Concepts in Biological Molecules
- 5.1 Macromolecules are polymers, built from monomers: Large biological molecules like carbohydrates, proteins, and nucleic acids are assembled from repeating monomer subunits.
- 5.2 Carbohydrates serve as fuel and building material: Carbohydrates, including sugars and polysaccharides, provide energy and structural support.
- 5.3 Lipids are a diverse group of hydrophobic molecules: Lipids, such as fats, phospholipids, and steroids, are nonpolar molecules with various functions including energy storage and cell membrane structure.
- 5.4 Proteins include a diversity of structures, resulting in a wide range of functions: Proteins, composed of amino acids, have diverse structures and functions, including catalysis, transport, and structural support.
- 5.5 Nucleic acids store, transmit, and help express hereditary information: Nucleic acids, DNA and RNA, store genetic information and play a crucial role in gene expression.
- 5.6 Genomics and proteomics have transformed biological inquiry and applications: Genomics and proteomics are fields that study genes and proteins, respectively, revolutionizing biological research and its applications.
Important Biological Molecules
- Carbohydrates: Serve as a source of energy and provide structural support. Examples include starch.
- Proteins: Have a wide range of functions, such as catalyzing reactions and transporting substances into and out of cells. Example is alcohol dehydrogenase.
- Nucleic Acids: Store genetic information and function in gene expression. Example is DNA.
- Lipids: A diverse group of molecules that do not mix well with water. Key functions include providing energy, making up cell membranes, and acting as hormones. Example is phospholipid.
5. 1 Macromolecules are Polymers, Built from Monomers
- Polymers: Large carbohydrates, proteins, and nucleic acids are known as macromolecules and are chain-like molecules.
- Monomers: These are repeating units that serve as the building blocks of a polymer.
Synthesis and Breakdown of Polymers
- Enzymes: Specialized macromolecules (usually proteins) that speed up chemical reactions.
- Dehydration Reaction (Condensation Reaction): A reaction in which two molecules are covalently bonded to each other with the loss of a small molecule, such as water.
- One reactant provides a hydroxyl group (-OH), and the other provides a hydrogen (-H).
- Hydrolysis: A process that is essentially the reverse of the dehydration reaction, where water breakage occurs. The bond between monomers is broken by the addition of a water molecule.
- A hydrogen from water attaches to one monomer, and the hydroxyl group attaches to the other.
Diversity of Polymers
- Cells have thousands of different macromolecules that vary from one type of cell to another.
- The inherited differences between close relatives reflect small variations in polymers, particularly DNA and proteins.
- The diversity of macromolecules in the living world is vast and effectively limitless.
- Polymers are constructed from only 40 to 50 common monomers and some others that occur rarely.
- Proteins are built from 20 kinds of amino acids arranged in chains that are typically hundreds of amino acids long.
- Small molecules common to all organisms act as building blocks that are ordered into unique macromolecules.
- Large molecules have emergent properties not found in their individual components.
Figure 5.2 The synthesis and breakdown of carbohydrate and protein polymers.
- (a) Dehydration reaction: synthesizing a polymer
The linking of two monomers/short polymer is done with dehydration by removing a water molecule, forming a new bond. - (b) Hydrolysis: breaking down a polymer
Adding a water molecule (Hydrolysis) breaks the bond between two monomers.
5. 2 Carbohydrates Serve as Fuel and Building Material
- Carbohydrates include sugars and polymers of sugars.
- Monosaccharides: The simplest carbohydrates or simple sugars, which are the monomers from which more complex carbohydrates are built.
- Disaccharides: Double sugars consisting of two monosaccharides joined by a covalent bond.
- Polysaccharides: Carbohydrate macromolecules are polymers composed of many sugar building blocks.
Sugars
- Monosaccharides: Generally have molecular formulas that are some multiple of the unit CH2O. Glucose (C6H12O6) is of central importance in the chemistry of life.
- Carbonyl Group (C=O) and Hydroxyl Groups (-OH): Trademarks of a monosaccharide.
- Aldose (Aldehyde Sugar) or Ketose (Ketone Sugar): Depending on the location of the carbonyl group.
- Glucose is an aldose; fructose, an isomer of glucose, is a ketose. (Most names for sugars end in -ose.)
- Monosaccharides are classified by the size of the carbon skeleton, ranging from three to seven carbons long.
- Hexoses: Six-carbon sugars like glucose and fructose.
- Trioses: Three-carbon sugars.
- Pentoses: Five-carbon sugars.
- Sugars vary in the location of their carbonyl groups, the length of their carbon skeletons, and the way their parts are arranged spatially around asymmetric carbons.
- Glucose and galactose differ only in the placement of parts around one asymmetric carbon, resulting in distinctive shapes and binding activities.
- In aqueous solutions, glucose molecules, as well as most other five- and six-carbon sugars, form rings because they are the most stable form of these sugars under physiological conditions.
Figure 5.3 The structure and classification of some monosaccharides.
- Trioses: three-carbon sugars (C3H6O3)
- Glyceraldehyde
- Dihydroxyacetone
- Pentoses: five-carbon sugars (C5H10O5)
- Ribose
- Ribulose
- Hexoses: six-carbon sugars (C6H12O6)
- Glucose
- Galactose
- Fructose
Figure 5.4 Linear and ring forms of glucose.
Chemical equilibrium between the linear and ring structures greatly favors the formation of rings.
To form the glucose ring, carbon 1 (magenta) bonds to the oxygen (blue) attached to carbon 5.
Monosaccharides, particularly glucose, are major nutrients for cells. In cellular respiration, cells extract energy from glucose molecules by breaking them down in a series of reactions.
Carbon skeletons serve as raw material for the synthesis of other types of small organic molecules, such as amino acids and fatty acids.
Monosaccharides are generally incorporated as monomers into disaccharides or polysaccharides.
Disaccharides
- A disaccharide consists of two monosaccharides joined by a glycosidic linkage, a covalent bond formed between two monosaccharides by a dehydration reaction.
- Maltose is a disaccharide formed by the linking of two molecules of glucose.
- Sucrose (table sugar) has two monomers: glucose and fructose.
- Lactose, the sugar present in milk, is another disaccharide, in this case a glucose molecule joined to a galactose molecule.
- Disaccharides must be broken down into monosaccharides to be used for energy by organisms.
- Lactose Intolerance: Common in humans who lack lactase, the enzyme that breaks down lactose. The sugar is instead broken down by intestinal bacteria, causing formation of gas and subsequent cramping. It may be avoided by taking the enzyme lactase when eating or drinking dairy products or consuming dairy products treated with lactase.
Figure 5.5 Examples of disaccharide synthesis.
- (a) Dehydration reaction in the synthesis of maltose.
The bonding of two glucose units forms maltose. The 1-4 glycosidic linkage joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. - (b) Dehydration reaction in the synthesis of sucrose.
Sucrose is a disaccharide formed from glucose and fructose. Fructose forms a five-sided ring, though it is a hexose like glucose.
Polysaccharides
- Polysaccharides are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages.
- Some polysaccharides serve as storage material, hydrolyzed as needed to provide monosaccharides for cells.
- Other polysaccharides serve as building material for structures that protect the cell or the whole organism.
- The architecture and function of a polysaccharide are determined by its monosaccharides and by the positions of its glycosidic linkages.
Storage Polysaccharides
- Plants store starch, a polymer of glucose monomers, as granules within plastids (including chloroplasts).
- Synthesizing starch enables the plant to stockpile surplus glucose.
- Starch represents stored energy, and the sugar can later be withdrawn by the plant from this carbohydrate "bank" by hydrolysis.
- Most animals, including humans, also have enzymes that can hydrolyze plant starch.
- Potato tubers and grains—the fruits of wheat, maize (corn), rice, and other grasses—are the major sources of starch in the human diet.
- Most of the glucose monomers in starch are joined by 1-4 linkages.
- The simplest form of starch, amylose, is unbranched.
- Amylopectin, a more complex starch, is a branched polymer with 1-6 linkages at the branch points.
- Animals store a polysaccharide called glycogen, a polymer of glucose that is like amylopectin but more extensively branched.
- Vertebrates store glycogen mainly in liver and muscle cells.
- Breakdown of glycogen in these cells releases glucose when the demand for energy increases.
Structural Polysaccharides
- Organisms build strong materials from structural polysaccharides.
- Cellulose is a major component of the tough walls that enclose plant cells.
- Plants produce almost kg (100 billion tons) of cellulose per year; it is the most abundant organic compound on Earth.
- Like starch, cellulose is a polymer of glucose with 1-4 glycosidic linkages, but the linkages in these two polymers differ.
- In starch, all the glucose monomers are in the a configuration.
- In contrast, the glucose monomers of cellulose are all in the B configuration, making every glucose monomer "upside down" with respect to its neighbors.
- Certain starch molecules are largely helical, fitting their function of efficiently storing glucose units.
- A cellulose molecule is straight, never branched, and some hydroxyl groups on its glucose monomers are free to hydrogen-bond with the hydroxyls of other cellulose molecules lying parallel to it.
- In plant cell walls, parallel cellulose molecules held together in this way are grouped into units called microfibrils.
- Enzymes that digest starch by hydrolyzing its a linkages are unable to hydrolyze the B linkages of cellulose due to the different shapes of these two molecules.
- Cellulose in our food passes through the digestive tract and is eliminated with the feces. Along the way, the cellulose abrades the wall of the digestive tract and stimulates the lining to secrete mucus.
- Some microorganisms can digest cellulose, breaking it down into glucose monomers.
Figure 5.6 Polysaccharides of plants and animals.
- (a) Starch
Amylose (unbranched) and Amylopectin (somewhat branched). - (b) Glycogen
Glycogen (extensively branched). - (c) Cellulose
Cellulose microfibrils in a plant cell wall and Cellulose molecule (unbranched).
Figure 5.7 Starch and cellulose structures.
(a) α and β glucose ring structures.
These two interconvertible forms of glucose differ in the placement of the hydroxyl group attached to the number 1 carbon.(b) Starch: 1-4 linkage of α glucose monomers.
All monomers are in the same orientation.(c) Cellulose: 1-4 linkage of β glucose monomers.
In cellulose, every β glucose monomer is upside down with respect to its neighbors.Another important structural polysaccharide is chitin, the carbohydrate used by arthropods (insects, spiders, crustaceans, and related animals) to build their exoskeletons.
Chitin is similar to cellulose, with B linkages, except that the glucose monomer of chitin has a nitrogen-containing attachment.
5. 3 Lipids are a Diverse Group of Hydrophobic Molecules
- Lipids are the one class of large biological molecules that does not include true polymers, and they are generally not big enough to be considered macromolecules.
- The compounds called lipids are grouped with each other because they share one important trait: They are hydrophobic; they mix poorly, if at all, with water.
- This behavior of lipids is based on their molecular structure.
- Lipids consist mostly of hydrocarbon regions with relatively non-polar C-H bonds.
- Lipids include waxes and certain pigments, but we will focus on the types of lipids that are most important biologically: fats, phospholipids, and steroids.
Fats
Although fats are not polymers, they are large molecules assembled from smaller molecules by dehydration reactions.
A fat consists of a glycerol molecule joined to three fatty acids.
- Glycerol is an alcohol; each of its three carbons bears a hydroxyl group.
- A fatty acid has a long carbon skeleton, usually 16 or 18 carbon atoms in length.
- The carbon at one end of the skeleton is part of a carboxyl group, the functional group that gives these molecules the name fatty acid.
- The rest of the skeleton consists of a hydrocarbon chain.
In making a fat, each fatty acid molecule is joined to glycerol by a dehydration reaction. This results in an ester linkage, a bond between a hydroxyl group and a carboxyl group.
The fatty acids in a fat can all be the same, or they can be of two or three different kinds.
The terms saturated fats and unsaturated fats refer to the structure of the hydrocarbon chains of the fatty acids.
- Saturated Fatty Acid: If there are no double bonds between carbon atoms composing a chain, then as many hydrogen atoms as possible are bonded to the carbon skeleton.
- Unsaturated Fatty Acid: An unsaturated fatty acid has one or more double bonds, with one fewer hydrogen atom on each double-bonded carbon. Nearly every double bond in naturally occurring fatty acids is a cis double bond, which creates a kink in the hydrocarbon chain wherever it occurs.
A fat made from saturated fatty acids is called a saturated fat. Most animal fats are saturated.
In contrast, the fats of plants and fishes are generally unsaturated, meaning that they are composed of one or more types of unsaturated fatty acids.
The process of hydrogenating vegetable oils produces not only saturated fats but also unsaturated fats with trans double bonds; trans fats can contribute to coronary heart disease.
The major function of fats is energy storage. A gram of fat stores more than twice as much energy as a gram of a polysaccharide, such as starch.
Figure 5.9 The synthesis and structure of a fat, or triacylglycerol.
- (a) One of three dehydration reactions in the synthesis of a fat.
One water molecule is removed for each fatty acid joined to the glycerol. - (b) A fat molecule (triacylglycerol) with three fatty acid units.
Figure 5.10 Saturated and unsaturated fats and fatty acids.
- (a) Saturated fat
At room temperature, the molecules of a saturated fat, such as the fat in butter, are packed closely together, forming a solid. - (b) Unsaturated fat
At room temperature, the molecules of an unsaturated fat such as olive oil cannot pack together closely enough to solidify because of the kinks in some of their fatty acid hydrocarbon chains.
Phospholipids
- Phospholipids are essential for cells because they are major constituents of cell membranes.
- A phospholipid is similar to a fat molecule but has only two fatty acids attached to glycerol rather than three.
- The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell.
- Typically, an additional small charged or polar molecule is also linked to the phosphate group, allowing formation of a variety of phospholipids that differ from each other.
- The hydrocarbon tails are hydrophobic and are excluded from water.
- The phosphate group and its attachments form a hydrophilic head that has an affinity for water.
- When phospholipids are added to water, they self-assemble into a double-layered sheet called a "bilayer" that shields their hydrophobic fatty acid tails from water.
- At the surface of a cell, phospholipids are arranged in a similar bilayer.
- The hydrophilic heads of the molecules are on the outside of the bilayer, in contact with the aqueous solutions inside and outside of the cell.
- The hydrophobic tails point toward the interior of the bilayer, away from the water.
- The phospholipid bilayer forms a boundary between the cell and its external environment and establishes separate compartments within eukaryotic cells.
Figure 5.11 The structure of a phospholipid.
- A phospholipid has a hydrophilic (polar) head and two hydrophobic (nonpolar) tails.
- This particular phospholipid, called a phosphatidylcholine, has a choline attached to a phosphate group.
- (a) Structural formula
- (b) Space-filling model
- (c) Phospholipid symbol
- (d) Phospholipid bilayer
Steroids
- Steroids are lipids characterized by a carbon skeleton consisting of four fused rings.
- Different steroids are distinguished by the particular chemical groups attached to this ensemble of rings.
- Cholesterol, a type of steroid, is a crucial molecule in animals.
- It is a common component of animal cell membranes and is also the precursor from which other steroids, such as the vertebrate sex hormones, are synthesized.
- In vertebrates, cholesterol is synthesized in the liver and is also obtained from the diet. A high level of cholesterol in the blood may contribute to atherosclerosis.
Figure 5.12 Cholesterol, a steroid.
- Cholesterol is the molecule from which other steroids, including the sex hormones, are synthesized. Steroids vary in the chemical groups attached to their four interconnected rings (shown in gold).
5. 4 Proteins Include a Diversity of Structures, Resulting in a Wide Range of Functions
- Nearly every dynamic function of a living being depends on proteins.
- Proteins account for more than 50% of the dry mass of most cells, and they are instrumental in almost everything organisms do.
- Some proteins speed up chemical reactions, while others play a role in defense, storage, transport, cellular communication, movement, or structural support.
- Enzymatic proteins regulate metabolism by acting as catalysts, chemical agents that selectively speed up chemical reactions without being consumed in the reaction.
- Proteins are the most structurally sophisticated molecules known.
- Proteins are all constructed from the same set of 20 amino acids, linked in unbranched polymers.
- The bond between amino acids is called a peptide bond, so a polymer of amino acids is called a polypeptide.
- A protein is a biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three-dimensional structure.
Amino Acids (Monomers)
- An amino acid is an organic molecule with both an amino group and a carboxyl group.
- At the center of the amino acid is an asymmetric carbon atom called the alpha (a) carbon.
- Its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a variable group symbolized by R.
- The R group, also called the side chain, differs with each amino acid.
- Figure 5.14 shows the 20 amino acids that cells use to build their thousands of proteins.
- The amino acids are grouped according to the properties of their side chains.
- One group consists of amino acids with nonpolar side chains, which are hydrophobic.
- Another group consists of amino acids with polar side chains, which are hydrophilic.
- Acidic amino acids have side chains that are generally negative in charge due to the presence of a carboxyl group, which is usually dissociated (ionized) at cellular pH.
- Basic amino acids have amino groups in their side chains that are generally positive in charge.
Figure 5.13 An overview of protein functions.
- Enzymatic proteins: Selective acceleration of chemical reactions.
- Defensive proteins: Protection against disease.
- Storage proteins: Storage of amino acids.
- Transport proteins: Transport of substances.
- Hormonal proteins: Coordination of an organism's activities.
- Receptor proteins: Response of cell to chemical stimuli.
- Contractile and motor proteins: Movement.
- Structural proteins: Support.
Polypeptides (Amino Acid Polymers)
- When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule.
- The resulting covalent bond is called a peptide bond.
- Repeated over and over, this process yields a polypeptide, a polymer of many amino acids linked by peptide bonds.
- The repeating sequence of atoms highlighted in purple in Figure 5.15 is called the polypeptide backbone.
- Extending from this backbone are the different side chains (R groups) of the amino acids.
- Each specific polypeptide has a unique linear sequence of amino acids.
- One end of the polypeptide chain has a free amino group (the N-terminus of the polypeptide), while the opposite end has a free carboxyl group (the C-terminus).
- The chemical nature of the molecule as a whole is determined by the kind and sequence of the side chains, which determine how a polypeptide folds and thus its final shape and chemical characteristics.
Figure 5.14 The 20 amino acids of proteins.
- Nonpolar side chains; hydrophobic
Glycine (Gly or G), Alanine (Ala or A), Valine (Val or V), Leucine (Leu or L), Isoleucine (Ile or I), Methionine (Met or M), Phenylalanine (Phe or F), Tryptophan (Trp or W), Proline (Pro or P). - Polar side chains; hydrophilic
Serine (Ser or S), Threonine (Thr or T), Cysteine (Cys or C), Tyrosine (Tyr or Y), Asparagine (Asn or N), Glutamine (Gln or Q). - Electrically charged side chains; hydrophilic
- Acidic (negatively charged): Aspartic acid (Asp or D), Glutamic acid (Glu or E).
- Basic (positively charged): Lysine (Lys or K), Arginine (Arg or R), Histidine (His or H).
Figure 5.15 Making a polypeptide chain.
- Peptide bonds are formed by dehydration reactions, which link the carboxyl group of one amino acid to the amino group of the next.
- The peptide bonds are formed one at a time, starting with the amino acid at the amino end (N-terminus).
- The polypeptide has a repetitive backbone (purple) to which the amino acid side chains (yellow and green) are attached.
Protein Structure and Function
- The specific activities of proteins result from their intricate three-dimensional architecture, the simplest level of which is the sequence of their amino acids.
- A functional protein is not just a polypeptide chain but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape.
- The amino acid sequence of each polypeptide determines what three-dimensional structure the protein will have under normal cellular conditions.
- When a cell synthesizes a polypeptide, the chain may fold spontaneously, assuming the functional structure for that protein.
- This folding is driven and reinforced by the formation of various bonds between parts of the chain, which in turn depends on the sequence of amino acids.
- A protein's specific structure determines how it works. In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule.
Four Levels of Protein Structure
In spite of their great diversity, proteins share three superimposed levels of structure, known as primary, secondary, and tertiary structure. A fourth level, quaternary structure, arises when a protein consists of two or more polypeptide chains.
Primary Structure: The primary structure of a protein is its sequence of amino acids.
- The primary structure dictates secondary and tertiary structure due to the chemical nature of the backbone and the side chains (R groups) of the amino acids along the polypeptide.
Secondary Structure: Most proteins have segments of their polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein's overall shape.
- These coils and folds, collectively referred to as secondary structure, are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acid side chains).
- One such secondary structure is the helix, a delicate coil held together by hydrogen bonding between every fourth amino acid.
- The other secondary structure is the β pleated sheet.
Tertiary Structure: Superimposed on the patterns of secondary structure is a protein's tertiary structure. While secondary structure involves interactions between backbone constituents, tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains (R groups) of the various amino acids.
- One type of interaction that contributes to tertiary structure is called—somewhat misleadingly—a hydrophobic interaction.
- Covalent bonds called disulfide bridges may further reinforce the shape of a protein.
Quaternary Structure: Some proteins consist of two or more polypeptide chains aggregated into one functional macromolecule.
Figure 5.18 Exploring Levels of Protein Structure
- Primary Structure: Linear chain of amino acids.
- Secondary Structure: Regions stabilized by hydrogen bonds between atoms of the polypeptide backbone.
helix and β pleated sheet. - Tertiary Structure: Three-dimensional shape stabilized by interactions between side chains.
- Quaternary Structure: Association of two or more polypeptides (some proteins only).
Sickle-Cell Disease: A Change in Primary Structure
- Even a slight change in primary structure can affect a protein's shape and ability to function.
- Sickle-cell disease is caused by the substitution of one amino acid (valine) for the normal one (glutamic acid) at the position of the sixth amino acid in the primary structure of hemoglobin.
- Normal red blood cells are disk-shaped, but in sickle-cell disease, the abnormal hemoglobin molecules tend to aggregate into chains, deforming some of the cells into a sickle shape.
What Determines Protein Structure?
- You've learned that a unique shape endows each protein with a specific function.
- But what are the key factors determining protein structure? You already know most of the answer: A polypeptide chain of a given amino acid sequence can be arranged into a three-dimensional shape determined by the interactions responsible for secondary and tertiary structure.
- If the pH, salt concentration, temperature, or other aspects of its environment are altered, the weak chemical bonds and interactions within a protein may be destroyed, causing the protein to unravel and lose its native shape, a change called denaturation.
- When a protein in a test-tube solution has been denatured by heat or chemicals, it can sometimes return to its functional shape when the denaturing agent is removed.
- We can conclude that the information for building specific shape is intrinsic to the protein's primary structure; this is often the case for small proteins. The sequence of amino acids determines the protein's shape.
Figure 5.19 A single amino acid substitution in a protein causes sickle-cell disease.
- Normal Red Blood Cell Shape vs Sickle-Cell
Protein Folding in the Cell
- Misfolding of polypeptides in cells is a serious problem that has come under increasing scrutiny by medical researchers.
- Many diseases—such as cystic fibrosis, Alzheimer's, Parkinson's, and mad cow disease—are associated with an accumulation of misfolded proteins.
- The method most commonly used to determine the 3-D structure of a protein is X-ray crystallography, which depends on the diffraction of an X-ray beam by the atoms of a crystallized molecule.
- Nuclear magnetic resonance (NMR) spectroscopy, cryo-electron microscopy (cryo-EM; see Concept 6.1) and bioinformatics (see Concept 5.6) are complementary approaches to understanding protein structure and function.
- These proteins, which may account for 20-30% of mammalian proteins, are called intrinsically disordered proteins and are the focus of current research.
Figure 5.21 Research Method X-Ray Crystallography
- Application: Scientists use X-ray crystallography to determine the three-dimensional (3-D) structure of macromolecules such as nucleic acids and proteins.
- Technique: Researchers aim an X-ray beam through a crystallized protein or nucleic acid. The atoms of the crystal diffract (bend) the X-rays into an orderly array that a digital detector records as a pattern of spots called an X-ray diffraction pattern.
- Results: Using data from X-ray diffraction patterns and the sequence of monomers determined by chemical methods, researchers can build a 3-D computer model of the macromolecule being studied.