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| Extended Lecture Outline |
Chapter 4: Polymers And Proteins |
4.1 Most biological materials are macromolecules constructed as polymers.
a. Macromolecules, very large, stable molecules, make up the bulk of every organism.
1. Biochemists and biologists often use the unit dalton (Da) instead of amu (atomic mass units) to relay information about a biomolecule's molecular mass. They do this to honor John Dalton, who was a pioneer in the development of an atomic theory of chemistry.
2. For especially large molecules, the unit kilodalton (kDa) is often used. A kilodalton is simply one thousand daltons.
3. Biologists generally choose a mass of about 1,000 daltons as an arbitrary dividing line between small molecules and macromolecules.
b. All macromolecules are made of small subunits covalently bonded in various combinations.
1. Macromolecules are called polymers where poly- means many and -mer means parts.
2. Monomers are the single subunits that are bonded together to form polymers.
3. Although thousands of different polymers can be found in a single cell, all polymers are constructed from a basic set of 30—40 different types of monomers.
4. Homopolymers are biological polymers made of only a single kind of monomer.
5. Heteropolymers are biological polymers made of many different kinds of monomers.
c. Polymerization is the process of synthesizing polymers.
1. Polymerization occurs when each subunit is linked to the next by removing a molecule of water. This chemical process is called dehydration synthesis or condensation.
2. Polymerization is an energy-requiring process.
d. Hydrolysis is the reverse of polymerization.
1. Hydrolysis (hydro- = water, lysis = splitting) is the process where water is added back to separate the subunits that have been joined by polymerization.
2. Digestion in humans is largely the process of hydrolysis. Humans consume food made of polymers and the body breaks the polymers down into monomers.
3. Three biological polymers and their monomers are extremely important in biology.
|
Macromolecule (polymer) |
Subunit (monomer) |
|
polysaccharide |
monosaccharide (sugar) |
|
nucleic acid |
nucleotide |
|
protein |
amino acid |
4. Lipids are the fourth most important building block for biological structure. Lipids are biomolecules that are not polymeric in structure. A basic lipid is made by linking three long hydrocarbon molecules, called fatty acids, to a molecule of glycerol.
4.2 Polysaccharides illustrate the concept of polymers as structural materials.
a. The function of a macromolecule is determined by its structure, and the structure is what suits each molecule for particular biological functions.
1. Polysaccharides are predominantly homopolymers comprised of simple sugar-monomers.
2. Simple sugars are often called monosaccharides.
3. Carbohydrate is another term used to describe sugars, used because the formula of a sugar is a multiple of CH2O, a "hydrated carbon."
4. Sugars are aldehydes or ketones (a compound with a carbonyl group, -C=O) that bear one or more hydroxyl groups (-OH).
b. Sugars introduce the subject of chirality and stereoisomers. Some carbon atoms can be oriented in two ways. With two choices at each position, there are several stereoisomers corresponding to each formula (Figure 4.1). All sugars have either the D or L configuration.
c. Closing the ring forms that some sugars assume (e.g. pentose, hexose) makes another asymmetric carbon. This leaves each sugar with alpha (a) and beta (b) isomers.
d. Simple sugars can be bonded in a glycosidic linkage by dehydration synthesis, removing a -H from one sugar and a -OH from the other to form water.
1. Sugars made of two simple sugars are called disaccharides.
2. Chains of up to ten sugars are called oligosaccharides. The smaller molecules are called complex sugars.
3. Molecules of more than ten subunits are called polysaccharides.
e. Since each sugar can be linked at several positions, several kinds of glycosidic linkages are possible. These are designated by notations such as a (1->4) and b (1->3) to show which carbon atoms are joined and whether the first sugar is an alpha or beta configuration.
1. Cellulose, which is found in the walls of plant cells, is the most abundant polymer on earth. Cellulose is made of D-glucose molecules joined by b (1->4) linkages (Figure 4.2).
2. Starch (amylose) is a homopolymer made of the same monomers that are found in cellulose, joined with a (1->4) and a (1->6) linkages.
3. Glycogen is polymerized glucose that is processed in the liver and muscles where it is stored energy.
4. Mucopolysaccharides are polysaccharide heteropolymers that are produced by animals with monomers of hexose sugars carrying sulfate and amino groups. Mucopolysaccharides form mucins, synovial fluids, and mucus (Figure 4.3).
5. Chitin is one of the most abundant mucopolysaccharides. It forms the cell walls of most fungi and the skeletons of arthropods.
f. Nucleic acids constitute the genome and the cellular machinery that translates information in the genome into cellular structures.
1. Nucleotides are the monomers of nucleic acids.
2. A nucleotide has three parts: a sugar linked to a ring-shaped, nitrogenous base and to a phosphate group.
3. A nucleic acid is made by condensing nucleotides into a chain, making bonds from sugar to phosphate to sugar to phosphate.
4. Nucleic acid has a sugar-phosphate backbone with the bases extending to the side.
5. Deoxyribonucleic acids (DNA) contain deoxyribose.
6. Ribonucleic acids (RNA) contain ribose.
4.4 Proteins, the most common biological polymers, have many functions.
a. Aside from water, the most abundant material in an organism is protein, which may be up to 80% of the dry mass.
1. Proteins form structures such as hair, fingernails, feathers, bones, tendons, ligaments, and skin.
2. Proteins effect movement since they are what actin, myosin, and tubulin are made of.
3. Proteins protect against foreign materials since an organism's entire immunological system is based on proteins called antibodies.
4. Proteins transport small molecules and ions through cell membranes, controlling the internal composition of a cell and what enters and leaves it.
5. Proteins receive stimuli and transmit information.
6. Proteins communicate messages between the cells of an organism. Hormones are an example of this.
7. Proteins such as hemoglobin carry and store material.
8. Proteins control or regulate processes such as genetic regulation and metabolism.
9. Proteins that catalyze chemical reactions are called enzymes. Enzymes increase reaction rate.
4.5 Enzymes are catalysts for chemical reactions.
a. Organic catalysts are called enzymes. Enzymes are highly specific and can only effect a particular molecule (or sometimes a few very similar molecules) known as the enzyme's substrate.
b. Inorganic catalysts like platinum are not very specific and are poorly suited to biological systems. The catalytic converter on the exhaust pipe of automobiles contains heavy metals such as platinum and palladium that catalyze the formation of carbon dioxide from oxygen and carbon monoxide.
4.6 The three-dimensional structure of an enzyme makes it very specific in the reactions it catalyzes.
a. Specific biological processes occur through the interaction of molecules that have complementary shapes, particular three-dimensional shapes that match one another like the shapes of interlocking jigsaw-puzzle pieces.
1. An enzyme interacts with its substrate at an active site, a pocket in the protein whose shape just fits the substrate's complementary shape.
2. A substrate enters an active site and is converted into a product which comes off the enzyme and leaves the active site ready to receive another substrate molecule.
3. Both the enzyme and the substrate change their structure during the crucial events of catalysis in the active site.
4. The product that leaves the active site may be quite different from the substrate that entered it.
5. Generalizing that all enzymes are proteins is incorrect. Ribozymes, comprised of ribonucleic acids, are also enzymes.
4.7 Proteins are polymers whose monomers are amino acids.
a. All proteins are linear polymers consisting of long chains of amino acids.
1. All known proteins in organisms use the same 20 amino acids as subunits (with only a few rare additions).
2. All 20 amino acids have the same general structure where a central atom, known as the alpha carbon, is bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a distinctive side chain (or R group).
3. The side chain (or R group) determines the identity of a particular amino acid.
b. In all amino acids except glycine, the alpha-carbon atom is asymmetric, since four different groups are attached to it.
c. Amino acids are grouped according to the nature of their side chains (Figure 4.4).
1. Eight amino acids have nonpolar side chains and are relatively insoluble in water.
2. Twelve amino acids have polar side chains and are hydrophilic.
3. Of the twelve amino acids with polar side chains, 7 are neutral, 3 are basic and 2 are acidic.
4. Proline is not actually an amino acid because its side chain is linked to its amino group. It is grouped with the amino acids because it is a common monomer of proteins and the cellular apparatus that synthesizes proteins treats it like an amino acid.
4.8 Amino acids are linked together by peptide bonds to form proteins.
a. Cells make proteins from amino acids by dehydration synthesis.
1. Water is removed from two amino acids and they become covalently bonded through a peptide linkage.
2. A chain of amino acids that is linked together by covalent bonds is called a peptide.
3. Every peptide consists of a covalently linked backbone, with a repeated -N-C-C-sequence formed by adjacent residues, and with amino-acid side chains extending from the backbone.
4. Two amino acids form a dipeptide, three form a tripeptide, a chain of a few amino acids is often called an oligopeptide, and a chain of many amino acids is a polypeptide.
b. A peptide chain has a direction because the two ends are different.
1. Peptides have a free amino group at one end called the N-terminus or amino terminus.
2. Peptides have a free carboxyl group at the other end called the C-terminus or carboxyl terminus.
3. The sequence of a peptide is always written from the N-terminus to the C-terminus. This is often indicated by an arrow in diagrams.
4. Cells synthesize proteins in the N-terminus to C-terminus direction.
4.9 Amino acids and proteins are commonly ionized.
a. At the pH typical of biological systems, close to neutrality, amino acids and peptides gain and lose protons (H+) and become ionized.
b. Acidic and basic amino acids have ionizable side chains that gain and lose protons within characteristic pH ranges.
c. The ionization of organic acids creates an ambiguity in nomenclature that can be confusing.
1. For example, glutamic acid is ionized with a -COO- group; the molecule is a base and is named glutamate.
2. The -ate ending is standard for the base forms of organic acids.
3. Examples of the pairs are: pyruvic acid/pyruvate; lactic acid/lactate.
d. Electrophoresis is a widely used technique for separating amino acids, peptides, and proteins based on their electrical charge and size (Figure 4.5).
4.10 The amino acids in a peptide are linked in a definite sequence known as the peptide's primary structure.
a. Frederick Sanger, around 1950 at Cambridge University in England, established some basic facts about the structure of the protein hormone insulin. He won a Nobel Prize for this work in 1958.
1. Sanger knew that insulin is a polymer of amino acid subunits.
2. He wanted to know in what order or sequence the amino acids were arranged.
3. Sanger showed that all molecules of each type of protein have the same unique sequence of amino acids.
b. Sanger developed a way to identify the amino acid in the N-terminal position of a peptide by binding an appropriate chemical reagent to it.
1. He found that glycine and phenylalanine are at the amino end of insulin and he concluded that insulin consisted of two polypeptide chains.
2. He treated the protein with mercaptoethanol, a compound that breaks disulfide bridges, a kind of covalent linkage that forms in proteins between two cysteine residues.
3. Two disulfide bridges hold the two peptide chains together while a third bridge links two cysteines on the same chain.
c. Sanger cut insulin into several small peptides with acid (which cuts proteins at random) and with digestive enzymes (which only hydrolyze peptide bonds between specific amino acids).
1. He separated these peptides by paper chromatography (Figure 4.6).
2. In paper chromatography, peptides are dissolved in a solvent and spotted on a piece of heavy filter paper.
3. One edge of the paper is placed in a solvent and as the solvent seeps into the paper, it carries the peptides along at different rates.
4. The separated peptides are located by spraying the paper with ninhydrin, which turns amino acids blue.
5. Each peptide is then hydrolyzed into its component amino acids. These amino acids are then separated by chromatography.
6. Spots of amino acids are identified by running other chromatographs with known amino acids to compare how they move.
d. Sanger identified the amino acids, and the N-terminal residues, in a set of peptides cut randomly from the protein.
1. He pieced together overlapping peptide sequences like a puzzle to determine the overall sequence of the protein.
2. He gradually reconstructed the entire sequence of both chains in insulin (Figure 4.7).
3. This work demonstrated that a protein has a unique sequence of amino acids which is now called the primary structure.
e. The technique of protein sequencing, applied to insulins from several species of animals, showed that these proteins have quite similar amino acid sequences, with only a few differences (Figure 4.8).
1. This pattern makes sense if all the tested species evolved from a common ancestor and accumulated small differences as they diverged from one another.
2. Comparisons of molecular structures like this help to establish the phylogenetic relationships among different species.
f. Sanger's primitive technique for determining the primary structure of a protein has been largely replaced by automated instruments that use the Edman degradation procedure developed by the Swedish chemist Pehr Edman.
1. Edman degradation removes amino acids one at a time from the N-terminus of the polypeptide and identifies them.
2. This procedure can determine the sequence of up to 60 amino acids in a short time.
g. The amino acid sequences of thousands of proteins are now known.
h. The amino acid sequence of each kind of protein is unique. All copies of the protein are identical because of the way that the sequence is genetically determined.
i. A protein may consist of more than one polypeptide chain. These chains may be held together by covalent bonds or by non-covalent forces such as hydrogen-bonding and other weak attractive forces.
4.11 Regular coiling or folding of a polypeptide chain determines the polypeptide's secondary structure.
a. Organic molecules can assume different conformations, or shapes, without breaking any of the bonds between atoms.
1. Proteins are held in a particular conformation by mostly weak bonds between the various atomic groups in its backbone and side chains.
2. These bonds stabilize the polypeptide into one of two general forms: fibrous protein or globular protein (Figure 4.9).
3. Fibrous protein is usually long and thin and is used mostly for structure.
4. Globular protein usually has a rounded shape.
b. Around 1950, the chemists Linus Pauling and Robert Corey examined the structure of fibrous protein by X-ray diffraction.
1. Pauling and Corey found that several proteins have the form of an alpha helix, an example of which can be found in Figure 4.9.
2. The shape of the alpha helix, which is maintained largely by hydrogen bonds between the carbonyl (-C+O) and imino (-NH) groups of the backbone, is one example of a protein's secondary structure.
3. Many proteins that constitute large parts of animal structure are little more than long alpha helices. Examples of these proteins are horn, hooves, porcupine quills, the myosins that make up parts of muscles, and the fibrin that forms blood clots.
4. Pauling and Corey used X-ray diffraction to describe a second conformation of proteins, the beta pleated sheet (Figure 4.9).
c. Collagen is the chief protein of some of an animal's toughest structures.
1. Bones, teeth, tendons, and skin are examples of structures that contain collagen.
2. Purified collagen fibers look like steel cables. They have a very specific banded pattern (Figure 4.9).
3. Each collagen fiber is made of many small units called tropocollagen.
4. Tropocollagen molecules consist of three polypeptides twisted around each other in a unique helical form.
4.12 Much of our knowledge of protein structure comes from studies of hemoglobin and myoglobin.
a. In the 1950s, X-ray diffraction was used to determine the structure of two closely related globular proteins: myoglobin and hemoglobin.
1. Myoglobin is found in muscle, hence myo- = muscle.
2. Hemoglobin is found in blood, hence hemo- = blood.
3. Both myoglobin and hemoglobin carry oxygen and become bright red when bound to oxygen.
b. Each myoglobin molecule (Figure 4.12) is a single polypeptide chain (of 153 amino acid residues) that folds up into the form shown in Figure 4.9.
1. About 75% of the chain is alpha helix and the helical structure is disrupted only where the molecule bends.
2. Certain amino-acid sequences tend to form alpha helices and others favor beta-sheets.
3. Computer programs based on known protein structures can now predict the likely structure of new peptide sequences with some accuracy.
4. Interactions between the side chains of a globular protein hold it in a particular three-dimensional shape known as its tertiary structure.
5. Because X-ray diffraction analysis is done by computer, the computer can be programmed to show the points where side chains interact.
6. Globular proteins tend to fold up with their polar groups on the outside in contact with the surrounding water and almost all their nonpolar groups clustered together inside, forming a hydrophobic core that is largely responsible for holding the protein shape (Figure 4.13).
7. Each myoglobin molecule contains a small heme molecule that serves as a prosthetic group.
8. A prosthetic group is a non-peptide molecule tightly bonded to the protein that is essential for its function.
c. Hemoglobin is made of four polypeptide chains, two alpha chains and two beta chains (Figure 4.9).
1. The alpha and beta chains have similar three-dimensional shapes and sizes.
2. The alpha chain contains 141 amino acids.
3. The beta chain contains 146 amino acids.
d. A protein made of two or more polypeptides has an additional degree of complexity beyond that of a single polypeptide. The quaternary structure of a protein is the form it has because of the assembly of its subunits.
1. Each polypeptide chain is called a protomer and the entire assemblage is a multimer.
2. The protomers are held together through interactions among some of their surface groups.
3. Many enzymes and other proteins function only as multimers.
4. All three levels of folding in globular proteins combine to establish the overall shape of the protein (Figure 4.14).
5. Globular proteins are often made of compact globular regions called domains that fold up independently of other such regions.
4.13 The primary structure of a polypeptide uniquely determines its three-dimensional shape.
a. Around 1960, Christian Anfinsen showed that RNase becomes enzymatically inactive when treated with chemicals that gently disrupt interactions among its amino acid residues.
1. Urea and guanidine hydrochloride will break the hydrogen bonds and other noncovalent interactions within proteins
2. Mercaptoethanol breaks disulfide bridges between cysteine residues.
3. When the chemicals disrupt bonds, the protein's shape changes. The protein is said to be denatured and is no longer active as an enzyme (Figure 4.15).
4. Proteins can also be denatured by heat. The most obvious example of this is cooking protein like that found in meat and eggs. This type of denaturation is not reversible.
5. Anfinsen found that RNase is reversibly denatured by chemicals and that when the chemicals are removed, the RNase is restored to its three-dimensional structure. The protein is said to be renatured.
b. Most proteins spontaneously assume their proper conformation, but others need some assistance in doing so. While they are being synthesized, these latter proteins bind to chaperonins, which are other proteins that prevent improper folding until synthesis is complete.
4.14 The structure of a protein is determined by the genome and shaped by evolution.
a. The genome of every cell in an organism contains the information for making all of the organism's proteins.
1. Information is required to specify one object out of a range of possible objects, and therefore an enormous amount of information is required just to specify the proteins of one cell.
2. The protein-manufacturing apparatus in a muscle cell follows molecular instructions that tell it to link certain amino acids in one particular sequence to form myoglobin.
3. Instructions from the genome also direct the amount of each protein made.
b. Cells contain the information for making myoglobin; this is because it enables them to make a protein with a very good shape for storing oxygen.
1. The information for making a functional myoglobin must have gradually evolved into its present form over many generations.
2. Mutations are always occurring in genomes, so some individuals will have instructions for making myoglobin molecules with minor variations in their sequences.
3. If any variations make individuals that are better adapted to their way of life, the offspring are more successful and the variation is passed on.
4. It is the whole organism that evolves, and the evolution of a single protein is just one aspect of the organism's evolution.
c. The variations that underlie evolution are the result of random mutations that occur by chance.
1. Many mutations are deleterious, while some turn out to be improvements.
2. Proteins are polymers and a mutation can change a single amino acid at a time.
3. The structures of biomolecules are determined by an organism's genome and are shaped into functional forms by evolution, through the selection of advantageous mutational changes.
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